Yeah, mods should be able to do that, but you're going to potentially run into a few problems. In some cases, ship variants are hardcoded into the game - the ones used in title screen, the tutorial, possibly a few other places. So if all of a sudden a ship hull doesn't have a weapon slot with the right id, there'll be explosions of the NPE variety. This is on my list of things to address - in fact, I was going to take a shot at it for 0.53.1a, but just not able to fit it in timewise. Ultimately, I'd like to get it to a point where a TC mod doesn't load vanilla assets it doesn't use.