japan is very nice place, I always travel with my son and daughter, i book twin room via jalan, not even once the hotel charge any surcharge.even 4 of us have breakfast in the hotel, they still allow us , no extra charge for my kids.
but mind you, even the hotel allow you to book twin room, if your kid is big enough, and difficult to share the bed, you better ask for extra bed, but the size of hotels in japan are overall small, not every hotel can allow extra bed, eg toyoko inn,