I've been lucky enough to go to Japan twice, and I envy you - it's a truly fantastic place for photography. The best thing is, they're such a huge nation of photographers themselves, that you'll never be looked upon as unusual on that front - possibly not even with a large format camera!
The first time I went it was cherry blossom season, which is a huge deal in Japan. We visited one temple in Kyoto where it was all lit up at night, and I couldn't get anywhere near the best viewpoints because of the hordes of photographers - and I don't mean snappers with tiny digi cameras, either. The majority of them had Hasselblads, Mamiyas and the like - as well as large format gear - and all on tripods. The likelihood of you getting into trouble for taking pictures is pretty small, I would imagine.
The other thing you needn't worry about is security. I've never felt as safe in any country as I did in Japan.
Have a fantastic time. Look forward to seeing some of the pictures!