Yeah, the reason most people don't have trouble with color blindness issues on AI War is that we specifically worked with colorblind players and solicited feedback until all of them were happy. Of course, there are so many kinds of color blindness that there's bound to be people falling through the cracks still. The art images are directly in the RuntimeData\Images\PlanetarySummary folder, though, so you can always edit their hue/saturation to your taste if you're unable to see them. That's maybe not the most graceful thing from a consumer standpoint, but I don't think there's any way to make it perfect for every kind of color blindness, and the flexiblity is at least there. Oh, and of course there are also the little patterns in the upper right corner of each panel that give a non-color-based indicator of what the ship type is.
In terms of the alphabetization, I should have mentioned that it's based on ship type name -- decloaker is of type tachyon beam emitter (given that it's function). It also shares a visual icon with the tachyon beam emitters, so that's part of why it's collapsed into that same icon on the sidebar. Most ships have the same type name as their individual ship name (fighter is fighter type, etc), but with some of the odds and ends that can get combined like you mentioned. Otherwise the sidebar tends to just explode with ship types.
As for the selected ships window, just select some ships and it appears at the bottom right area of the screen. It shows text names of ships, not combined, alphabetized. Clicking any line item in the list selects just those items. Shift plus right-clicking any item in the list removes that item while keeping all the rest. Etc.
And Nalgas is quite right on the warp gates -- look for the Warp Gate - Full or Warp Gate - Warp Only abilities on ships (as opposed to Warp Gate - Reinforce). Only a few have it, and AI Eyes and Warp Gates are the main ones.