I don't think I've ever seen a three-prong outlet in Japan (maybe only new installations?), but "earth screws" are quite common (any room prepared for an air conditioner will have one at least) http://www.hakusui-trading.co.jp/safety/img/img02.jpg
What's the point?
I think it's just a legacy thing - historically, the only things that needed grounding were static appliances like fridges, washing machines and air conditioners. The manual in our fridge has this instruction for earthing http://mayoyo.tokyo/jIe.jpg
I need to revise my comment that "I don't think I've ever seen a three-prong outlet in Japan", because now that I have power sockets on my mind, I just saw a three-prong outlet at my gym. So I guess newer buildings have them.