I've taken such trains more than once, much more than once, and never actually encountered anyone who who talked on the phone at all hours of the night. You're right, it might happen.

As or border crossings, in the old days I would give the conductor my passport in the evening and get it back in the morning. Not often nowadays, thanks to the Schengen agreement. But no border guard has ever woken me up. (Edit: For scale, I think I've entered ten different countries on night trains, no idea how many trips in total.)