Is it only certain ship components (engines, computers) that get automatic replacements in current design specs, or is there a way to get the game to automatically "refit" all designs with the optimum combination of new weapons, shields, and "extras" (extended fuel cells, etc)?

And how come I can't have more than one Colony Base type on a ship in MoO 1? I have to have separate designs for tundra, dead, inferno, and regular Colonies.

In MoO 1, nothing gets updated on ships except range, though a design will get cheaper as you research higher techs. There's no way to refit old ships; you just have to design new models and scrap the old ones (or use them for second line/security, etc.)

MoO 2 ships automatically get the newest engines and range increases. Anything else means redesigning and refitting (done through the production queue).

With the colony bases in MoO 1, the higher level ones will work for that planet type and all below, so a Barren colony base will also let you colonize Standard worlds and Tundra covers Tundra, Barren and Standard, etc. The best way of dealing with this is to just design a new colony ship with your most advanced base type as your research progresses.

In Moo2, ships are automatically equipped with the best of everything if you deselect tactical combat.

Well, they're equipped with what the computer thinks is the best, and if you've ever seen the ships the AI Empires field .....