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.