Maybe it was the boys having a midnight snack and they just don't want to tell you. I would prefer to think that rather than a rat or an animal. Or a poltergeist for that matter.
I bought about 300g of ham one day (I put it in a plastic container that night before going to bed) and woke up in the morning to make the girls sandwiches and more than half of it was gone. But that was in the fridge so it had to be a person. They all swear they didn't eat it but I have caught DD2 gobbling down a handful of ham before so I think it was her.
I used to have a boyfriend who was on stillnox. He regularly would get up at night and eat vast quantities and claimed to have absolutely no memory of it the next day. After losing several whole tubs of connoisseur this way we broke up.
Could someone be sleep walking? (but the bones missing is weird)