In Manhattan they're mostly running a 4-track system, so they can easily shut down half the tracks for maintenance while maintaining 24/7 service. I think they've got other problems.
For alternative examples: BART is not 24/7, and possibly sucks even more than MTA. CTA's 2 main lines are 24/7, but it's nearly 100% a 2-track system, and its biggest problem (IMO, anyway) is that the arrangement of seats inside the cars is so very desperately bonehaded.
