I've only worked at two Japanese companies. My wife has worked at several in her life (and loves her current company and job). I've also read stories of people in bad places asking for advice. I'll answer based on that, but realize that it is not a huge sample size.

"black companies" are very much a thing and take advantage of those that either can't (or feel that they can't) find other work. Recent years have seen laws to reform the number of hours worked and against various forms of "power harassment" (you can google that for what it is, but basically managers/superiors cannot do certain things). My first company in Japan kinda waffled between a company with a ton of overtime, got quite nice, and then went back the opposite direction.

Some of it is just social pressure, which is a big thing in Japan. People don't want to rock the boat, so they will, for example, clock out but keep working, not leave before the boss, etc. Corona causing a lot of people to work from home has changed things, though, and a lot of people who have gone back to the office have a much better understanding of how much useless BS there is and how many hours of their lives they're missing out on. We'll see how it plays out in the future.