Japan is good fun! I'm currently studying here.
In Jokoji's case, it was mostly bad luck and changing tastes. Its entire existence was based on the success of a hotel called Chitosero, which opened sometime in the interwar period, on the banks of the river that runs through Jokoji's centre. Being 30 minutes' train ride out of the big city of Nagoya, it's easy to imagine how popular it was, in a time before cheap air travel. However, like most of the developed world, as people became more affluent after WW2, the Japanese started to head further afield for their holidays, and Chitosero eventually closed in 2003. Incidentally, the empty building is still standing despite the best efforts of arsonists and vandals, and is also a great photo opportunity (I'll pop a shot in at the end of this post). With all of the tourists, and consequently all of the money, now gone, all that is left in Jokoji is one cafe (which has had no customers both times I've visited) and the temple that gives the village its name - the 'ji' in Jokoji is given by a character which means 'temple' in Japanese and Chinese.
Chitosero (sorry about the blown sky, the harsh winter light couldn't be rescued in Camera RAW)