I often question if its not the body shop. Ive heard plenty of stories where a car is dropped off, and then it takes months, sometimes years to get it back for whatever reason, and by the time its returned parts are removed.
I saw something like this on Judge Judy one day. If the body shop took possession of it, theyre responsible for any stolen parts while its in their custody. The only other way to prevent this is to give the body shop a completely stripped car to work with.