If they want, that we hunt the NPC (which is fine with me, even better), then the mission must count, if we catch him/her, no matter where. Also I think it is better when NPCs also flee - but not every time. This is very annoying, especially for players with a bit unstable connections. We all know that flying in one system usually works, but jumping to another system (=instance) may fail.
The mission should also state, that the target may flee and should be hunted - this to inform the player, that he needs a Wake Scanner, not necessarily default for each combat ship, especially not for the smaller ones.
And NPCs which stop random pilots with an interdiction should either never flee, or they need to be saved too. And if the NPC flees to another system, it should be theoretically possible to follow it, but if not done the NPC should be deleted. It is extremely annoying if you have 3 interdictions, and damage the NPC every time and it is back in 15 seconds - did not happen to me, because mostly I win interdictions, but I have read about that too.
I do not understand that a modern and well designed system like ED does only have 'ghosts' instead of NPCs, which are objects as long as they are needed. This problem seems to introduced by an AI which now also flees. Maybe this should be changed until the system is able to do it right. It is not so important that a NPC 'gets away', because he only has a ghostly temporary existence.