I wish I could just remove them altogether in Retribution... currently, they're just glowing textureless balls until I find a more convenient way to "hide" them from recordings. Same with colony ships and the other fare.
Well unless you need the AI to actually produce ships (i.e. you spawn ships in the dev exe instead), perhaps you could just give them an absurd research requirement which effectively locks those ships out from play, as the AI will not be able to research something that costs millions.