Pretty sure there aren't microwaves in the rooms (from memory). Just a small fridge. However there is a small convenience store next door, and they heat meals that you buy from them (like most stores in Japan).
Hi Carrrolinee, I wish I could remember!! My first impression remembering back to April was no there weren't any. However, I will check my pictures and update the answer if there were. The English of the staff in this hotel is quite limited if sending them a question.