> The biggest cities in the world does not have overnight sub, and they carry far more people around the city, is that a problem? No, of course not.
I don't think we want to use Guangzhou, Shanghai, Nanjing, Delhi, Jakarti, Beijing, Mumbai, São Paulo, or Lagos[0] as models for New York City's transit. A casual observer might claim Tokyo is a decent model, except that Tokyo is structurally a radically different city, to the point where the comparison doesn't provide much of value.
> The cost of overnight running, does it justify the value?
It absolutely does. Shutting down the subway overnight would cripple the entire city. Even though overnight service is limited compared to daytime service, it's an essential part of the city's infrastructure.
Moreover, eliminating overnight service isn't actually necessary for providing the improvements that the subway needs, so talking about eliminating overnight service is a red herring.
[0] the nine cities in the world, excluding Tokyo, whose metropolitan area is larger than New York City's.