They can and do fly dark on missions, but not in high air traffic areas like airports, where they need to be transponding for safety to avoid mid-air collisions. If you go look at P8 and Rivet/Cobra flight paths, you will see them transpond for a few minutes before/after landing/takeoff but the majority of their flight path is dark.

They would need a really, really good reason (not saying it doesn't happen, just doesn't happen without cause) to takeoff/land while dark.