Could it be possible that Mr. Mooney was an experienced serial killer who mentored a young Joe? Many fans really like the idea of this theory, and even the ones who think it’s unlikely still know there's something sinister about Mooney’s character.
There’s a scene where Joe shows Paco the book vault and explains how to properly care for the old, limited edition books. This is intercut with flashbacks of Mooney giving Joe the same speech when he was a teenager. This shows that Mooney taught a lot to Joe, and it’s obvious that Joe sees himself in Paco and tries to protect him.
But maybe this wasn’t all Mooney taught Joe. He was the one who Joe confided in when he killed Elijah and his response was “some people deserve to die.” Perhaps Mooney had a code of conduct for such a situation, because he also told Joe exactly what to do when this happened.
There is also the fact that Joe mentions the door in the book vault was built for cash transactions, but we never see it used in this way, even in flashbacks of Mooney. Plus, the vault is soundproof so it could be that Mooney used it in the same way that Joe did.
Whilst Mooney had strict rules for protecting the beloved books, he still trapped Joe in the vault on more than one occasion, so we know that he’s capable of at least that.