Sounds like another case of payment processors wanting to fuck shit up in places they have no business doing anything, from what I could get from the article.

既に絶版となったマンガを中心に、まだ電子化もされていないようなレアな作品群を無料で再び読めるようにし、その作者に十年以上も広告収益を還元し続けた「マンガ図書館Z」でしたが、近年は（カード会社など）決済サービスの面で対応に苦しむことが増えてきました

Translation mine:

Many manga are now unfortunately going to fall out of print, with no way for many to accessibly read them. The creators whose works were published on this site tried for more than ten years to enable this venture to succeed, but in recent years, card companies (among others) made doing so impossible.