I lived up in Washington Heights for a couple years so I spent a lot of time in the 168th St. station. I'm not certain how deep it is, but it's definitely much deeper than your normal subway station. They used to have this slow, human-operated elevator and the door had a small window. You'd watch the elevator shaft moving in front of you and it always felt like you were descending into the coal mines or something.

Let's not forget the logistical difficulty in moving lots of people around. If hundreds of airline passengers can be stranded out on the tarmac for a very long time in winter weather, it's certainly not beyond reason for subway passengers to be stuck underground or on an overhead section for a long time, too.