I hate to be the cynic, but have you considered predators of the two-legged variety? Is it possible that someone may have stolen them out of spite/hunger/envy? Sometimes people can be just as wily as natural predators, unfortunately. In all likelyhood it's probably not a person, but it doesn't hurt to look at your coop/yard security from all angles.
Good luck, and please keep us posted with any updates!
Good luck, and please keep us posted with any updates!