The Masamoto shop definitely does not. The Aritsugu shop does. I can't recall 100% but I am reasonably certain Nehoni does not. You will likely solve your ATM issue if you go to a 7/11. It is not widely known amongst the locals but foreign cards do not work in most Japanese ATMs. The machines in the 7/11s are all set up for foreign cards. If that fails give your card issuer a call. The transaction may be blocked at a security level.