tarrith It's been 9 months since the last message on this post, and 5 full updates have gone by since; You'd be much better off just creating a new post for future reference, as this breaks the 15th forum rule pretty badly.
To answer your question though, the game's graphics are incredibly lightweight, so on most modern computers you'll always be CPU limited rather than GPU limited. Cosmoteer tries to process each ship on a different thread for performance's sake, but it'll ultimately be limited by the largest ship, and possibly the 'master' process thread if there is one (I'll have to check with the dev, I don't remember and I'm curious now). Really the more stuff you have on screen the more the processor starts falling behind, and therefore the GPU usage goes down in turn.