1)You reshuffle after each scavenging run. The FAQ entry is in the extremely unlikely event you exhaust the deck mid-run.
2)Yes, bars etc are map cards. You check if they are even allowed at your location, then if so they sit in the exploration box with residents encountered etc. and may be attempted or completely ignored if you like untill the end of the run when they get shuffled back into the exploration deck. (See top of each map card for details)
Gotcha on #1. So it's there in case you go through a bunch of extra cards that add to the unknown deck and you run out
#2. Makes sense. For some reason I thought they would block from exploring the unknown if you couldn't bypass them but looking again, there is nothing that says that. So you just leave it in the explored area and can ignore or attempt them. Cool