I am hoping the current USS spawning system is placeholder, until proper missions and events generated from the background sim are in. At least it would make more sense for an NPC to be generated in a station or other system nearby when you accept the mission and fly to where you may be expecting them. Loads better than them magically appearing.
Maybe when persistent NPC's are implemented this will be fixed.
At the moment this is the one aspect of the game that does feel like just another MMO mission spawning grind mechanic rather than a manifestation of the background game universe, and for this game that is a real shame.