What why? O_o
Not that I'll miss them I guess...

Very good question.

From MaGog's logs for 24 May (part 2 of 2):

NOTE! Probably CHANGED FILE Master of Orion: Collector's Edition [In Dev], all_files, Windows installer, English (part 1/2 of 2), dl_ver: 43.6.1.0.20804 (gog-15) ***TO*** 44.4.1.1.22707 (gog-16)

NOTE! Probably REMOVED FILE Master of Orion: Collector's Edition [In Dev], all_files, Patch 43.6.1.0.20804 (gog-15) [Windows]

NOTE! Probably CHANGED FILE Master of Orion: Collector's Edition [In Dev], all_files, Mac OS X installer, English, dl_ver: 43.6.1.0.20804 (gog-16) ***TO*** 44.4.1.1.22707 (gog-17)

NOTE! CHANGED Master of Orion: Collector's Edition [In Dev], changelog (http://www.an-ovel.com/downloads/chg/chg_1456225523.htm)
NOTE! ADD +++ Patch 44.4.1.1.22707 (24 May 2016)
NOTE! ADD +++ Greetings Explorers,
NOTE! ADD +++ Today marks the release of version 44.4, known as Early Access phase 4. The focus of this build was polish and improvements based on your feedback, so read on for the patch notes! We will have a progress update from the dev team later today, so stay tuned for that.
NOTE! ADD +++
NOTE! ADD +++ General
NOTE! ADD +++ Starting Age option added to match setup (Options: Pre-warp, Post-Warp and Advanced)
NOTE! ADD +++ Production speed and Population growth speed options added to Advanced section of match setup
NOTE! ADD +++ Savegames are now ordered by date
NOTE! ADD +++ Added new galaxy model to reduce brightness of the core
NOTE! ADD +++ Removed mouse drag in match setup
NOTE! ADD +++ Added new text to the GNN news ticker
NOTE! ADD +++ Added Host Migration timeout (15 seconds) to multiplayer and an error message to allow players to continue the game in single player mode
NOTE! ADD +++ Optimized batch rendering; Reduced vert counts drastically improving performance in lower end systems
NOTE! ADD +++ Fixed issue where Quick match AI players were not being properly loaded, resulting in only AI present regardless of Galaxy size
NOTE! ADD +++ UI tweaks for both tactical and ship design tooltips
NOTE! ADD +++ Added graphical indicator for non-assimilated pop in colony management
NOTE! ADD +++
NOTE! ADD +++ Gameplay & Balance
NOTE! ADD +++ Colony ship, Troop Transport, Civilian Transport and Space Factory blueprints are now auto-upgraded.
NOTE! ADD +++ Moved one of the Technological Victory buildings from Moleculartronics to Multi-Dimensional Physics technode
NOTE! ADD +++ Re-balanced planet composition (improved algorithm for diminishing returns)
NOTE! ADD +++ Silicoid Population growth speed reduced
NOTE! ADD +++ Uber-planets have been adjusted to play more like the Gaia biome
NOTE! ADD +++ Races with Uber-planet perk now start the game in a planet with the Biome they can Uber-terraform
NOTE! ADD +++ Additional wormholes added to Circular Large and Circular Huge galaxies
NOTE! ADD +++ Troop Transports no longer remove marines from the colony
NOTE! ADD +++ Increased minimum number of shares desired by races for better balance of the GMF
NOTE! ADD +++
NOTE! ADD +++ Diplomacy
NOTE! ADD +++ Diplomacy balance update to improve strategic decision-making of AI
NOTE! ADD +++ Made it less likely that the AI will reject reasonable deal proposals
NOTE! ADD +++ Tech trades: Made it less likely that the AI will also offer credits as part of trade
NOTE! ADD +++ Improved analysis for Candidate Ally selection (both Defensive & Offensive)
NOTE! ADD +++ Tech can now only be traded with races with which you have a good disposition
NOTE! ADD +++
NOTE! ADD +++ Espionage
NOTE! ADD +++ Acquire Data mission now reveals all current colonies of target
NOTE! ADD +++ New mission: Steal Charts
NOTE! ADD +++ New functionally allows queuing future missions
NOTE! ADD +++ Added queue info to spy mission description
NOTE! ADD +++ Overall missions duration adjusted
NOTE! ADD +++ Revolt mission effect now last 20 turns
NOTE! ADD +++ The camera no longer automatically changes zoom level or centers on a spy when selecting them
NOTE! ADD +++ A "spy location" button has been added to the Espionage window allowing you to quickly switch the camera to the colony the spy is located at
NOTE! ADD +++
NOTE! ADD +++ Artificial Intelligence
NOTE! ADD +++ Improved efficiency for Production
NOTE! ADD +++ Improved offensive and defensive strategies
NOTE! ADD +++ Improved planetary ratings and potential colonization awareness
NOTE! ADD +++ Improved Engage command to allow for multiple actions in the same turn (i.e. Engage and Bombard)
NOTE! ADD +++ Defensive fleets now take into account immediate hostiles and empire under threat scenarios
NOTE! ADD +++ Uses radars to determine settlement orbital defenses if possible
NOTE! ADD +++ Added Blockade and EngageToBlockade targets
NOTE! ADD +++ Changed engage distance for bombarding pirate settlements from Distant to Neighbors
NOTE! ADD +++
NOTE! ADD +++ User Interface
NOTE! ADD +++ New multiplayer top bar added
NOTE! ADD +++ Improved Match Setup screen
NOTE! ADD +++ Improved Ship Design Screen
NOTE! ADD +++ Race information panel added to Audience screen
NOTE! ADD +++ Improved Espionage screen
NOTE! ADD +++ Improved Invest pop-up
NOTE! ADD +++ Fixed Build pop-up alignment and added minor improvements
NOTE! ADD +++ Establish Embassy deal renamed to Accept Embassy
NOTE! ADD +++
NOTE! ADD +++ Tactical
NOTE! ADD +++ Range Dissipation and Armor Penetration now affect Weapon Damage
NOTE! ADD +++ Increased the size of battlefields
NOTE! ADD +++ Fixed multiple bugs and Improved Overall performance
NOTE! ADD +++ Fixed several modifier bugs and reworked the Continuous Fire mod
NOTE! ADD +++ Added a simple Tactical Tutorial
NOTE! ADD +++ Implemented AI Groundwork for Opening Moves and added new Targeting Profiles
NOTE! ADD +++ Fixes and tweaks on tactical intro
NOTE! ADD +++ Ships no longer attempt flanking maneuver against structures
NOTE! ADD +++ Reduced size of Pirate Ship collision box by 50%
NOTE! ADD +++ Fix for collision check parameters for asteroids and added a safeguard condition to choose which behavior to use
NOTE! ADD +++ Added a base accuracy for energy weapons
NOTE! ADD +++ Re-balanced DPS and Ship Survivability
NOTE! ADD +++
NOTE! ADD +++ Ship Design
NOTE! ADD +++ Tooltip upgrade showing HULL SPACE USED.
NOTE! ADD +++ Fix for creating new ships, now the screen handles the info properly
NOTE! ADD +++ Fix for attack rating scale factor
NOTE! ADD +++ Fixed typos and made improvements in weapon and module descriptions
NOTE! ADD +++
NOTE! ADD +++ Localization
NOTE! ADD +++ Several fixes on dialogues and descriptions
NOTE! ADD +++
NOTE! ADD +++ Sound Effects
NOTE! ADD +++ Meklar Emperor SFX added
NOTE! ADD +++ Emperors' audience SFX added
NOTE! ADD +++ Audio notifications for Spies added
NOTE! ADD +++ More audience sounds added and updated for all races
NOTE! ADD +++
NOTE! ADD +++ Notable Bug Fixes
NOTE! ADD +++ Fixed exception caused by selecting Build on a Worker Ship when is about to merge with another ship.
NOTE! ADD +++ Fixed softlock when ordering a Spy to Hold.
NOTE! ADD +++ Fixed a softlock in the tutorial after switching planets with the keyboard arrows.
NOTE! ADD +++ Fixed the Buy button not always working properly.
NOTE! ADD +++ Fixed freeze when trying to use the "Stasis Field" special (special not yet implemented)
NOTE! ADD +++ Fixed the battle with the Orion Guardian lasting forever when simulating certain scenarios.
NOTE! ADD +++ Fixed the emperor's voice not stopping when skipping the Council
NOTE! ADD +++ Fixed bug in Tech tree that caused some Tech Nodes to appear as locked when they were in fact available
NOTE! ADD +++ Fix for tactical weapon tooltips and combat speed tooltips from enemy ships
NOTE! ADD +++ Optimization fixes to Navigation Caches and AI_CanTravelTo/Fleet's FindPath
NOTE! ADD +++ Fix for items missing when upgrading blueprints
NOTE! ADD +++ Fixed incorrect Pollution perks descriptions
NOTE! ADD +++ Fix for a blueprint sometimes becoming overweight after autoupgrading
NOTE! ADD +++ Fixed two AI asking for Share Charts at the same time
NOTE! ADD +++ Fix for diplomatic deals spamming when the first one is invalid
NOTE! ADD +++ Fixed update for blueprints not showing when discovering a new computer
NOTE! ADD +++ Crash on early game when reaching unknown civilizations
NOTE! ADD +++ Fixed biological bombs so they don't affect Attack Rating

the Superfrogs are indeed missing when searching the catalogue ...

Damn. I guess I should have gotten Superfrog at some point. :/

If GOG were to remove any game from the catalog, I'd expect them to announce it properly and publicly. So before indulging on some weeping and gnashing of teeth, I'd wait a little while in case this has only been a technical error and the Superfrogs re-appear as if nothing had happened.

Scratches was removed last year and there was not a single comment from the GOG staff.

Really? Not cool, GOG, not cool at all...

(I only remembered the Duke Nukem and the Descent games, and IIRC, there was a public statement by GOG about the situation. That's why I assumed they would do the same in other similar cases)

It's kinda like roulette; you aren't 100% sure how GOG will react with the removal of the game. Sometimes, they will announce it a good period of time before it actually occurs (ARMA series, Original War), other times they will announce a bit before removal (Blade of Darkness), in some cases they will announce it at the time of the removal (Descent), some other times they will announce it after prodding from forum members (Space Rangers) and other times they utter not a single word about it (Chessmaster 9000, Scratches).

Yeah, still sucks though.
Especially since they rarely if ever come back.
I can only remember Fallout and the Nordic games coming back.

This is quite understandable, but I still believe it appears more professional if we learn about it in the first place from someone blue, rather than from someone who is merely blue-eyed.

This too.
There should be an announcement ready the moment of or soon after removal.