I guess it depends on the region. My cousin and family live near Hiroshima and they say they see more and more abandoned houses around them. My guess is they are getting cheaper and cheaper. But I wouldn't be surprised if around historic sites like kyoto some savvy investors are buying old charming houses, renovating them and reselling them for a profit. What area are looking into? If you are aiming for the countryside I would say you don't have to worry too much about prices.

With all the attention they've been getting in other countries lately (see the number of youtube videos for example) it's possible the prices are going up a little bit.