As for the locks disapearing the above stated reasons are the most likely ones for them disapearing.

However, from antedotal evidence and some strong comments I have heard from friends who are TSA and Airport Police the most likely reason is that TSA didn't reattach the lock or just cut them. From what they have told me is that there are a number of screeners who don't bother with finding the TSA keys for the locks and just cut them off. There are others who simply forget about the locks or remove the key from the lock and discard the lock. In theory the TSA key is not supposed to be removed without lock being relocked, but in reality that isn't what can happen. Also from the TSA folks here, it seems that TSA is running out of the forms saying we said hello to your luggage. So they are not putting them in all of the bags. (Now I don't know if the forms are running low, or the screeners are too lazy to go get more forms when they run out).

As for losing locks to the baggage system, it is a possibility, but more likely it was TSA.