I guess you can broadly split compliance work like this into two categories, spot checks and audits. The former where you're pseudo-randomly checking that they are following the rules, and punishing them where you aren't (taxes work like this), the latter where you are systematically checking that the rules have been followed (I believe building inspections work like this).
1 inspector/100 facilities seems within the realms of reason if you're doing spot checks. It's absurd if you think you need to be doing continuous audits.
It sounds like you're saying there's good reason to think the slaughterhouse business needs the latter (that there is a documented history of abuse despite them happening - I don't really know anything about the industry), but most industries seem to survive on spot checks.
I don't know much about the zoos and breeders that the USDS is inspecting either, maybe continuous auditing would be a good idea, but it doesn't seem absurd to think that spot checks are sufficient. Is there some particular reason to think that they're like slaughter houses and that spot checks are clearly insufficient?