JCB cards are widely accepted in Japan. You should be okay with your Discover card. The only problem is that most merchants in Japan do not know the fact that Discover cards can be accepted through JCB terminals. They would most likely reject Discover card without even trying to scan your card. Do ask them to try Discover card.

JCB terminals also accept American Express cards.

I am still surprised at the hotel not accepting Visa and MC. It is probably a temporary problem that their processing machine may have been used for fraud or something.