As I recollect, civilians can be designed with their own Jump Drives, and that they can use the jump drives of anything sitting on a point.
The new version of civilian ships design themselves based on your tech levels. I may be wrong but I also believe that civilian ships will only route through permanent jump gates, so while they can technically traverse using a jump drive in practice they won't visit colonies without permanent connections.
And I've seen NPRs use the squadron jump to land quite a distance away, so decent sensors would be smart.
Oh yes, I guess it depends on your definition of decent sensors. Of course if they squadron jump that far away then plasma and HPMs on a station aren't going to be much use.
Also the shielding is probably for when so many NPR ships jump through, you can't kill all of them before they reactivate. Also, they can move while jump blind, just not see or shoot.
This is actually a rather interesting question (to which I don't know the answer). If I'm guaranteed the first shot (or several shots) then that clearly shifts the offense to defense balance, but how much?