I feel as though a good way to implement NPCs--in regard to ones that try to emulate players--is for them to simply be passive ships; no pirating, policing, or mercenary NPCs. NPCs could be more of an aesthetic filler, spawning idly and moving from point to point, perhaps having some defensive capabilities but never to go on the offensive.
I suppose the issue that could arise from this is if you destroy one, would you be allowed to extract resources from them in the form of pirating cargo or salvaging hulls. This could make for semi-interesting gameplay, but could also just become a way people farm for quick resources instead of fighting other players for them or gathering them independently.
I feel in the end it comes to how many players are able to be in one shard/server, and how often they're online. If there's an abundance of players constantly having the opportunity to bump into each other, then I see no reason to have ship or character NPCs; but if it takes a good hour before you might have even the opportunity to intentionally find another player, then I think it'd be good to implement some filler here and there to make the world seem less lonely.