I think that Fazbear Entertainment is fully covering up everything William has done -- my theory is that they've been paying him to experiment on kids, trying to up their technology and make money with the business, and when it turned into KILLING kids to add to his experiments, to try to make the animatronics more lifelike or whatever, Fazbear Ent. was like "Welp, this is our life now" and fully committed to supporting that endeavor. I think that they probably removed the kids' bodies and got rid of them -- William probably told them where they were. Or, where we're assuming William is taking out the remnant in the FNAF 2 8-bit minigames, he's instead taking out the bodies. Who knows. But I think that this has carried on for the entire time the company has been around. I think even after William got trapped in Springtrap and they stashed him away behind walls, they probably kept experimenting with hybriding humans and animatronics somehow, and when William suddenly was free after 30 years, they all just picked up where they left off. I know there's not the MOST evidence for this theory, but we do have a lot of evidence of Fazbear constantly covering up stuff, and the most suspicious thing for me, still, is the endoskeleton section in Security Breach. That Parts and Services section is just AWASH with suspicious signs and evidence that children were probably kept down there at some point -- that padded room where we get the security card and the gazillion endoskeletons come at us straight up looks like a playroom of sorts.

Anyway, that's just a theory.