You’ll probably want to message damdai, kuroppi, and nohoho, since they’ve all traveled to Japan and are kind of in-the-know as to where to go, along with which Japanese players speak English in order to help better accomodate you.
Based on this article there are a few places that seem good:
HEY in Akihabara. Only 10yen/play for ST, but there’s only one machine, and it seems to be more of a beat-em-up and schmup place.
Royal in Nakano. 3 H2H setups, 50yen/play, and good competition on Thursdays. The very same place that puts out those Nakano Royal videos.
Gamespot Versus in Nishi-Nippori. East v. West battle on Tuesday all day, and Danisen ranking battles on Saturday. Normal price is 50/play, but on Tuesdays, it’s 50yen/2play, and you play your opponent a 2/3 set. I guess this is a good spot for ST players, since we always see matches of their battles every week on the supersf2turbo YT channel.
Mi-Ka-Do in Takadanobaba 500yen/freeplay on Thursdays starting at 7pm. Normal price is 50yen/play. Lots of strong competition, and Mattsun works there. One of the premiere destinations for ST.
I haven’t heard of an arcade open 24:7.