Places will enforce it - I'd say most do not - but my sample size is only large enough to say confidentially that the places my friends went to do not, with one exception that enforced it.
Source: Friends with tattoos who have visited Japan as I don't have any myself.
E: This is one of very, very few shows I'd ever recommend and it covers this topic: https://www.viceland.com/en_us/show/needles-and-pins , specifically the ones in Japan and South Korea which have very similar culture surrounding tattoos.
I went to a public onsen in Hakone. More like a western spa than a bathhouse. They made me purchase a covering for my leg tattoo, even though I am not Japanese and therefore could never have been Yakuza.
I was also in Hakone, last month. There was a foreigner with pretty obvious tattoos on his body in the onsen I went to. It probably depends on the bathhouse.
The Japanese culture is also extremely conformist and rule following.
In my (limited) experience the letter of a rule is very important while the intent of the rule is not considered much.
I'd expect the rule to be enforced but I don't _really_ know.