It is my understanding from the Mastercard, 7-11, and JP Bank announcements that EMV cards are blocked at ALL atms in Japan. If this is indeed the case (I don't have an EMV card to test with) then this absolutely leaves people stranded.
Normally this wouldn't have too much fallout as people could make other arrangements, however, it seems that there may have been very little lead time between the announcement and the actually termination of service which didn't give people enough time to prepare.
I only have a maestro and an Amex card, both issued from europe.
Can you not use your AMEX normally or arrange a cash advance on that card? They are not affected by the mastercard issues.
and any clue how long this will take?
I haven't seen an expected end date. For now I would assume that it is indefinite.
Also, in general I suggest people just get used to carrying cash around (again).
If you are in country and no longer have access to your bank account then this may not be an option. Try to use other cards as much as possible, but if you are truly stranded try calling mastercard's Japanese emergency line to see if they can issue you an emergency (non-EMV) card which should still work in Japan, or an emergency cash advance.