i didnt notice any difference between any of the ships at all, handling and speed has been identical.

not that i care much anymore what with a proper flying mod:

http://nomansskymods.com/mods/fly-it-like-you-stole-it/

With the best pulse upgrade I get 220 within planetary. Don't know what the dropship is, I'm guessing those larger ships? I ONce I had one, but I don't remember having a better speed without upgrades.

This ship:
http://imgur.com/a/CZt58

I'm going to check some more. And it has damaged pulse-upgrades, so might be they're still counting, and so on.

But it just seemed so strange - I fully upgraded a scout and barely broke 220u (240u when the planet proximity is off). And this one is faster on normal pulse, even if it turns slower..

Did some more testing. It's just a bug - the critically damaged pulse-upgrades still work :) Order or placement of pulse-upgrades also doesn't matter, and gives no link-bonus (including the pulse-engine block - no bonus). Top speed when planet-inhibitor kicks in is 220.

Imo, they really should change this somehow - give some ships higher cruising speeds out of the planet inhibitor, that sort of thing.

Anyway. So if you put the pulse-upgrades in between random free blocks, they work exactly the same.

Ship behavior, including speed and velocity etc.. controlled by a global xml file in one of the .pak files. So any difference among ships regarding performance is an illusion or perhaps a bug.
I can see someone switching ships and somehow the game doesn't register, that the newly acquired ship doesn't have the same upgrades as the previous ship and the game continues to give the same benefits for the new ship, like the previous -higher upgraded- ship. I'm just theorizing, after I noticed, that sometimes things gets "stuck", in lack of a better way to describe, when lot's of things happen and messages are delayed.
For example, I was shooting asteroids for minerals, but at the same time I ran a scan, while I came under attack by pirates. Things got hectic, so I began landing on the planet I was next to. As soon as I land, I clicked on the flag radar thing to claim discovery.
The game was still listing the minerals I picked up in space and it took a good 20 seconds to go through all the messages including the pirates scanning me, the planet name and climate and the "restore point" , while I was already walking around the planet.