Do carriers such as Janet Airlines carry ADS-B transponders?
You can just look them up. Here's a screenshot from Flightradar24 taken at about 1410 UTC on 22 May 2017.

I imagine in an emergency they'd be given priority just like any other aircraft in distress. The crew might have specific orders covering that situation that requires them to head for a military base. Their operation is so secret, though, that I doubt we'd find out unless a emergency occurs.