Why does such a troubled metro still run 24/7? Most of the best-performing metros in the world (HK, SG, Tokyo) close at midnight.
Also note that the MTA's troubles have nothing to do with running the system 24/7. The subway has run 24/7 for a century, and for most of that century maintenance was not a problem. What happened recently was that the state started cutting the MTA's subsidy, so maintenance started to slip and the system fell apart -- something which happened in the 1980s, but people have no ability to learn from past mistakes.
Where I live is an example of that: during weekdays the light rail closes IIRC between midnight and 6, they only keep it running on weekends because of all the people going out at night (the metro always runs but that's fully automated). Just because the bus system isn't enough to handle a city's peak load, it's usually fine for handling the load on periods where the load is the smallest.