I've noticed that after a while, my civilian ships start to cause some lag - not much, but it mounts up. I understand that the civ-ship spam will be fixed for 6.4, but for the moment, are there any penalties for simply executing civilian ships?
Secondly, what's the best way to go about it? I can field a basic ship, but I can't see any way to target the civilian ships. However, i do remember reading something about grabbing them with a tractor beam?