kodos96:

If this were the real explanation though, then it would mean that the vast majority of criminals go free, since in the real world there is rarely "slam-dunk" evidence.

I don't know much about the specific example of Japan, but generally speaking, this comment isn't necessarily correct. In a culturally homogeneous and tightly-knit society, in which strong traditional norms covering all aspects of life are taken with great seriousness and individuals normally don't spend much time in isolation and anonymity, it can be very hard to commit a crime without leaving slam-dunk evidence. Moreover, in such societies, it may be that only a vanishingly small number of people would be capable of committing a crime and lying convincingly about it when questioned later by authority figures.

To what extent the contemporary Japan has these characteristics, I don't know, but I'm pretty sure that it has them in a greater measure than, say, the U.S. I also don't know if there could perhaps be some other aspects of their culture that have similar implications for the issues of crime.

Therefore, even if it's true that Japanese courts are nearly always agreeing with prosecutors doesn't by itself mean that the system is worse than the American one by either metric. We would need more concrete data to make such judgments.