It sounds as if no one really knows and/or there was a cover up. I doubt any police force would use cadaver dogs if they didn't think it necessary.
There are most certainly failings in terms of child care / protection.
At one end, there would seem to be a few untrained but goodhearted people who were doing their best and, at the other extreme, child predators and general sadists, with everything in between.
I don't find it reasonable for any police force to simply dismiss rumours of suspicious disappearances or descriptions of potential murders. On the other hand, thorough desk research of records and cross-referencing witness statements (including the credibility of each), and the history of the place might have eliminated the need to gut the place.
At the moment (and I still have more reading to do), I get the impression that there may well have been a cover-up of some of the abuse. Some of that could turn out to be deliberately covering up for sexual or harsh physical abuse, and / or, concerning physical abuse, a dismissive (ultraconservative) attitude to child welfare and discipline.
In one or two of the accounts in the itv updates, the children's accounts of sexual abuse were acted upon - but only to dismiss the adult in question. One at least then went on to abuse at least one other child. In one case, it was the victim's father who didn't want the head of the home to involve the police for some reason, perhaps simply to protect the child's privacy... no idea.
I do hope that this inquiry will help to bring closure to the victims. It's expected to carry on for another year, so time will tell.