I believe Disney would have to pay them something if they elected to accept DDP. The actual restaurants in Japan do accept DDP. However, since the food service areas in the Japan pavilion are not operated by Disney, they may choose to accept or not accept dining credits, and the status of snacks can change anytime.
Even Disney-operated food service areas have been known to discontinue DDP snacks without notice (like the make your own treats at Goofy's or the ice cream sandwiches in Dinoland)