This game probably just suffers from the classic syndrome of slowing down when there's a whole lot going on. I made a custom star system with 6 stars and well over 100 planets, and after a little while when there were decent sized fleets moving around my fps began to noticeably drop now and again when moving the camera (though a slight drop at the time, I have seen a youtube video that purports to have 1000 scout cruisers, and the fps is well below 1.0