It's my understanding that small to medium sized cities (and rural areas) depopulating is going on now throughout almost all of Japan. One of the things that really surprised me recently is how low the cost of real estate is for an older, normal middle class home in some sparsely populated areas of Japan.

Apparently the declining population and younger people not wanting to live in their parents' rural countryside home is having a significant effect on property values.

I wouldn't let this get in the way of going there though. Kumamoto is a very nice prefecture to see. They will rebuild (again) and it'll continue to be a great place.