They are also doing massive upgrades and maintenance on the L line, but the J/M/Z parallels much of the L's route.
This is fine, it makes sense to do that. It is not as useful to shut the entire system down each night. It makes much more sense to shut parts of it down piecemeal.
NYC's subway network is vast. It actually used to be three different systems that were merged together. The numbered and lettered lines have separate maintenance facilities and hardware.
What's truly unique about NYC's subway, is how redundant it is. Most neighborhoods are serviced by more than one line. When I lived in Washington Heights (northern Manhattan) the 1 line needed emergency maintenance when a roof in a station collapsed, and I believe that reconstruction took almost a year, but the A/C parallels the 1 by only a few blocks.
I don't think you're right about this. There's just a lot of maintenance work that needs to be done that can't be done even with slow-moving trains going by a few times an hour. Signals need to be replaced, rail surface need to be smoothed, ballast needs to be cleaned and redistributed, ties break and need to be replaced, signals need to be replaced, etc. London and Hong Kong crews can do something like replace a section of rail overnight. It's very hard to do that in NYC.