One of those days any of "monster girl" series will explain why they weren't hunted down, if not for their differences then for the simple fact that having an absurdly strong "human-like" species is a danger to our survival.
You might as well ask, "What happened to the other human species?" or "Why haven't we hunted down the other great apes?" in our own world. Our forebears lived with and sometimes against Denisovans and Neanderthals (as evidenced with the DNA of both mixing into our modern genomes), and while the physical anatomy of Denisovans is unclear, Neanderthals were definitely physically stronger and more resilient than the average
sapiens sapiens.
While the great apes are much more distant cousins, chimps (vanilla and bonobos), orangutans, and gorillas are all absurdly strong when compared to humans.
In both cases, if I had to hypothesize a guess...isolation. Modern humans spread out better and survived whatever hard times our more isolated cousins couldn't in the last fifty-odd-thousand years, while the same isolation sheltered the great apes from the fearful human societies of the last five hundred-or-so years.
Were "genjin" real, they likely survived to the present day by being intentionally isolated and keeping a low profile. Individual demihumans might be adopted by or trade with human communities, but genjin villages would be like Ogami's...hard to get to and off the beaten path, in mountains, deserts, rain forests, and the like so that they largely stayed a "rumor", like the chimpanzee or gorilla until the mid 1800's. And paleontologists would have a field day, because for every species or subspecies of genjin that made it to the Reiwa, there might be five or six that didn't, because of said isolation and small populations.
