The NPC in the shop is like the bounty board- you go to it and select a quest. With the "NPC going up to you," I mean an NPC flies up to your base and starts bothering you find his ship/rescue someone/avenge her planet/whatever.
Ehh, it shouldn't happen too much, and you should have an option to automatically ignore all hails anyway, if you're busy building or something...Yes ! Imagine you, standing at your medium-sized space station... Doing some building work or upgrades on your docked ship... Then a strange vessel appears and contacts you and gives special quests with story-sense...