Usually, if a non-looping subways hit EOL, there will be a sweep and a rest period. Looping subways might just change drivers and keep going...well, it can suck when you are on a train that is retiring (in Beijing, they just dump you out and tell you to wait for the next train...).
Generally this is a short rest period, ~ 10-15 minutes max during peak times and 30 minutes max otherwise. Nobody's kicking you off, you can just wait until the train starts back the other way.
It's also generally the least busy part of the line.
The second greatest problem on NYC's subway for people who wish to "live" there (after rush hours) has to be the light. The fluorescent is unavoidable.
Or the train is being removed from service. That's not really going to happen in the middle of the night but definitely happens during times when they are decreasing service (after rush hour, after like 11pn)