[m4rtink]

One general side effect is harder access to affected regions - with less people to serve public transport gets reduced or even abandoned entirely (affect rail lines the most, due to the necessary maintenance needed for safe operation). IIRC there are numerous rural lines scheduled to be closed in the near future in Hokkaido for example (and of course a bunch of them got abolished in the Yubari area).

Is this a problem ? I guess not really & it might actually help the nature regenerate in those areas.

Where it can be a bigger problem is various small islands - where the islands being inhabited makes a big difference in territorial claims & is a very important thing in regards to what China has been doing (building artificial islands, etc.). For that reason I suspect the Japanese government subsidizes island communities quite heavily to keep them going & keeping suverenity over those islands and the surrounding sea.