Using Booleans in TS for ships is only a bad thing if you just stick two things together and expect it to work. You have to do a lot of work welding vertices and straightening up the mess Booleans make if you want to use them. However, many (if not all) of my recent ships make use of Booleans, and they are not having serious problems. The main trouble is that you can't mirror an object and stick it flush with the other side (for reflecting down the ship's spine) as TS Booleans won't work if a line on one object intersects a line on the other object. Or if you are trying glue to non-planar faces, or a number of other conditions. Play with them for a while, and see what comes out. Oh, and Boolean union in TS does remove geometry, where the ships overlap. Trouble is, you usually wind up with a face containing a hole or you get an unnecessary edge deleted (thus creating a face with at least one angle greater than 180 degrees), and that is what Freespace REALLY doesn't like.
