One of the reasons many people consider the New York City subway to be the best in the world is that it's one of only a handful of rail systems which operate all night, every night. It provides service to every station (except one in the financial district), although many routes change and most service operates every 20 minutes. Most cities shut down their rail systems overnight so they can perform essential inspections and maintenance. Check out this recent documentary by Boston's MBTA showing all the work they do in that short window from about 1-5 AM.
Since the MTA New York City Subway runs all night, maintenance work requires careful planning and frequent diversions, and occasionally replacing a line segment with shuttle buses. There are limits to the work you can do when trains are operating, raising the costs of repairs and increasing the risks related to the safety of workers. The same service changes often happen repeatedly as bits of work are completed.
Last year the MTA rolled out its Fastrack program which shuts down a line segment completely for a few consecutive nights and floods it with employees to do maintenance and repairs. Get in, finish, get out. Now they are expanding it beyond Manhattan.
The concept of focused complete shutdowns is gaining traction in transit agencies all over North America because of the reduced length and cost of construction. For example, Boston is closing a major downtown station for two years rather than the six years it would take to complete renovations while keeping it open. Sometimes you may need shuttle buses (preferably at night when the streets are empty, or otherwise with temporary bus lanes); other times you can get away with using a temporary platform.
As long as the inconvenience is small and well publicized in advance, a shutdown makes so much sense than to drag out repairs.