I think civilian ships are any that are neither pirates or authority vessels, so anyone who isn't wanted or the cops counts as a civilian. That's who I've been blowing up for the hunt civilians missions.
As for the Mineral Magpie, I think these are random encounters where a ship will buy a certain commoditity at above market value. Never come across one myself, but I think you need to be carrying that commodity when you meet them in order to sell to them. I think they're placeholder for something more complex later.