It happened to me last year during Golden Week so not that much has changed. I should have known better because I'd seen ATMs turned off during public holidays before. I even had large hotels refuse to accept credit cards but eventually I found accommodation and a restaurant that accepted Visa.
Ironically it happened to me today (which is a holiday in Japan). The ATM at one of the convenience stores wouldn't connect to my bank after 5pm. Luckily the ATM at the convenience store right beside it was working...
Over the last few years 24/7, 365 days/yr ATMs are have become much more common. As have ATMs that accept foreign banking cards. As has a more generalized acceptance of CCs.