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.