Must be a quirk for those cards in Japan. I've had no problems using my Canadian cards in Japan, and don't recall ever having to sign. In terms of banking and payments, it has improved a lot over the years: ATMs are mostly 24/7, or at least you can always find one, banks don't shut down over holiday weeks anymore (some do occasionally but it's a one-time thing for big upgrades for interoperability), and you can use credit cards and tap-to-pay almost everywhere. My only complaint is the sheer number of digital payment options. You end up with using at least 1-2 on top of your credit card because it's tied to some other service.
I don't know much about CC, but possibly difference of PIN method can be a reason. Possibly like merchant only support offline PIN vs your card only support online PIN?
All my cards have an IC, however they were Australian cards. Perhaps it's an additional step for foreign credit/debit cards?