I hope some move back. From what I've seen/heard, the countryside is suffering radical population shifts. The following article has some great graphs to illustrate the point. There is a giant dip in the 20s (school) and a terrifying peak in the 55-60 range. But the greatest disparity is that there are many many more old (70s) than teenagers in the countryside. Across the nation those two groups are roughly equal.
Japan has a immense centralization of jobs in Tokyo (and to a much lesser extent Osaka). It's "go make your fortune in New York", but 10x as extreme.
They've been talking about the need to decentralize for decades now. The earthquake showed the risk of centralization and having a single point of failure for the economy and the government (famously, some foreign companies moved HQ and/or datacenters to Osaka). Nothing has changed though. If anything things are becoming even more centralized.
There has been minority political endeavors talking of introducing the concept of "States" to Japan to structurally support this sort of decentralization. At times attempts have come close to fruition (most recently Hashimoto's attempt in Osaka), but none have borne fruit.
http://www.tofugu.com/2015/03/06/japanese-countryside-emptyi...