There is no ban in Japan, just a recommendation by the FSA(Financial Services Agency) and so far no one has followed it. From your linked article:
Unfortunately, Coincheck and Monex already delisted all three currencies a while ago. So far, they are the only companies to do so.
So, two exchanges delisted XMR (and others) but not related to this FSA recommendation because it was before that.
So, writing XMR banned on more and more exchanges is clearly exaggerated for dramatic effect.

Also the coincheck (and perhaps Monex) delisting is probably related to the coincheck hack (as Ive read somewhere). Something about them being afraid that the privacycoins could be used to obfuscate the stolen NEM. Perhaps that decision even influenced the FSA in their recommendation.