Interesting discussion.

I know that in Stockholm there is no technical reason for the subways to close after midnight - which they do. They used to run all night (though they did not run often in the middle of the night), but a couple of years ago they decided to stop. It was a mixture of preventing crime, preventing homeless persons to sleep in the subway stations, making maintenance easier and the general urge to look like they were doing something. The night-time bus drivers were not so happy about it.

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In NYC the lines are typically four track in the inner parts of the city with a local and express, splitting off into two track on the outer edges. So what you get is that for a month or two a part of the line is express or local only on weekends and/or late nights for maintenance and repairs. On the two track lines they'll sometimes shut them down entirely late nights for maintenance. But there's no conceivable reason why you would need to close the entire system at nights.