Been to Japan a few times. The trains are camera friendly. As are most of the people. Key is to smile and be friendly. Once even had a street punk show off his modified cadillac. I saw it parked outside a fast food restaurent and started snapping. He saw it, stepped outside the restaurent, got in the car, turn on the engine and showed me all the funky modified suspensions. The car can hop on its wheels. Hahaha!
The only time I was stopped was while I was taking pictures in Tokyo Hands. Apparently, its becoz they won't want you to take pictures of its products and prices. The staff was very friendly when asking me to stop taking. Even apologise to me. Didn't ask me to erase or anything. That's what I call service.
Do enjoy your stay there. Its a nice country to visit.