If NPC's where persistent, encounters would be so rare we would see threads about how there is no risk to mining, no risk to trade, and nobody to blow up for the pirates and bounty hunters. If you had the population of the whole game mining in a planetary ring evenly spread out you probably would not see anybody. NPC spawning is triggered by player presence, otherwise the server would be processing 99% useless information.
I agree with the original poster; Frontier had something of the same issue, but NPCs (while never absent) did seem to become rarer the further you got from human space. NPCs should be spawned according to rules more sophisticated than 'players are nearby' (and yes, I'd love the idea of persistent NPCs that act with concern for their own survival and can conceivably be encountered repeatedly - for example if they're pirates focusing on a particular asteroid belt, or traders who've established a specific route that you can track).
NPCs of different types should usually only spawn in plausible situations - pirates don't make any sense in areas nobody visits or passes through (as even if they run across explorers they aren't going to be carrying cargo worth seizing), traders make no sense too far from trade routes etc. Leave danger in the great unknown to occasional explorers competing for your discoveries, NPC aliens or the much more occasional outcast. And almost all of those are stretching it when you're looking at spawns around black holes or the like.
For all that we've only seen Thargoids as aggressive aliens in past incarnations, Elite established a whole host of alien races in its setting. If you read the backstory, apparently they all mysteriously left the galaxy shortly before the events of Frontier, but perhaps some could return as fortune-hunters?