It's more than restaurants choosing to limit it, a straight up ban has gone into effect for the last 9 months now [1] - hence it's much better than before. Not sure how or if it's legal, but some divey spots have managed to get exemptions or are just risking it though - a friend of mine who runs a cafe says that the cafe is classed as some kind of social club so it's not subject to the same ban, but that sounds pretty shakey lol.

[1] https://www.japantimes.co.jp/news/2020/04/01/national/japan-...