Welp, I have nothing new to offer with NPRs. I imagine that when you add a system, it's not possible for an NPR to generate there, but I'm not sure.
Anyways, about missiles, it might refer to the chance to hit targets moving at a certain speed. If your missile has a high speed and agility, it will have a better-than 100% chance to hit something moving much slower. You can imagine anything above 100% as just being 100%, if it makes you feel better.