All things considered...yokai are generally a bunch of assholes, with the 'good' ones being rare exceptions. I mean, with humans as the majority and a bunch of shape-shifting, human-eating almost-immortal monsters as the minority, yeah, no shit humans would want to have a way of keeping track of them. It's not some secret police tasked with picking out ethnic minorities. It's a bunch of murder-hobos tasked with killing monsters who want to stay invisible and unknown for some edgy, possibly dangerous reason.
Just my thoughts though. Don't know why everyone else is so enamoured with a clean, happy fantasy world without discrimination. Maybe it's the modern sensibility.
Actually a good number of traditional youkai are harmless or even beneficial. Many serve as guardian spirits and have temples.