Not sure what the concern is for the subways... Might be some flooding in a station or two, but safe transport during the raging storm above. Why state they are closed (hype-ing the sotrm?), when with an observer (presuming he/she is awake) at the front of every train to monitor presence of water, they could just shut down sections as needed.
So that train can't go forward. It can't go backward because there are trains following. Now everyone is stuck on that line.
Parts of the subway are well over 100 feet below ground. Water has to be pumped out and with heavy rains, they are overwhelmed. Water and the 600 volt third rails don't mix well, either. The signals can also short out. If the pump system goes out, you're going to get dead people.
Read this story from four years ago: http://cityroom.blogs.nytimes.com/2007/08/08/why-do-the-subways-flood/