I've never been, but I know the stores there sell lots of freshwater plants, they are some of the best (and most expensive) set ups for their plants that I have ever seen, there is a store in San Francisco that sells Amano style tanks and a 20 gal set up with the Co2 and lighting is between $2000-3000 for the equipment. I don't know of saltwater stores, or corals, but when you get there I'm sure you can ask the locals for coral shops. If you get a chance go to the big public aquarium, it has some of the biggest and best coral tanks in the world, including the first tank with whale sharks in it.
As far as diving, again local help would be invaluable, they have really strange rules about diving and the northern islands are cold. that doesn't mean the diving is not good, just be prepared. If you do get down to the southern islands by Okinawa the diving is tropical and has many fish that are rare in the hobby, should be a great place to dive, and one of the few places I have not been that I really want to go.
