Yeah, I've noticed this as well. They not only slowly close old stations, but they almost stopped building new ones since about 2007.
I don't understand why people downvote your comment. It isn't like you're forcing them to have babies and do something about the world by stating the fact about Japan's decline
The "decline" you mention is privatization of JR and their efforts to make it more profitable. Privatization started in 1987, but it wasn't fully privatized until 2006.
If it has anything to do with babies, you have your cause and effect reversed. Autos are a cause of declining birth rates...
https://www.journals.uchicago.edu/doi/10.1086/731812
So a reduction in trains causes a reduction in birth rates, not the other way around.