Oh, I agree they suck. The first ships I designed were Fast Colony Ship, Fast Constructor, and Fast Survey Ship. I figured I wanted them there FAST (plus, I wanted to toss a little extra colonists into the colony ship, and a few more sensors and more range into the survey ship; does the constructor benefit from more modules?). I still want the option of making them...
As for checking each tech in the tech tree, the problem is five turns (or ten or twenty...) later when it becomes time to select the next tech. At that point, I've forgotten what techs I need for each ship.

(Memory isn't my strong point...)
So most of those ships the AI makes are custom?