Baggage handlers steal stuff, too. I'm not trying to defend the TSA, but you don't know it was them. I had a pocket knife and some video game stuff stolen out of my bag once. Ir was years ago, before TSA existed.
If it's valuable, carry it with you. Or ship it UPS or FedEx with lots of insurance.
And that's how they get away with it, too - whoever's actually doing it. They (whoever "they" are) won't permit cameras to be installed in the areas where inspections are done and baggage handled, and since there's no chain-of-custody, Team Sexual Assault and the baggage handlers each get to say, "Nuh-UH, wasn't US! Anyways, you can't prove anything! Talk to the other guys!", and at best, you're looking at an enormously-long time to work through the system and maybe get whatever "they" think you might get back for your loss. Maybe the person(s) responsible gets written up (won't lose his or her job, though), probably not. You might, possibly, get back a quarter what the stolen item was worth, in a couple of years, barring some miracle.
Granted that TSA has been proven to DESERVE being monitored continuously while on the job (I'm reminded particularly of the guy who "lost" an Ipad going through the line, but had the find-me feature turned on; he got a news team to track it to the guy's house, and set off the alarm while they were talking to him on camera at the front door, denying everything. Dude had specially-made pockets to steal stuff like that sewn into his uniforms) - but so have many baggage handlers. Could be either; could even be both. And they'll NEVER permit such monitoring to be instituted.
And just saw the update - glad you didn't lose your stuff after all. I stand by my comments, regardless.
When I fly, I usually pack in my checked bag a multi-tool of some kind, a locking blade Victorinox Swiss Army knife, and a locking folder, like the RAT-1. All relatively inexpensive, so I won't cry if they disappear. The SAK I put in my toiletries bag. The multi-tool goes in a shoe. The folder goes in another shoe. And I usually stick a pair of socks in the shoe after the knife is put in. My thought is that it's legal, but it's going to make the thief work harder to rip me off.
As for locks, interesting side note. My son was asking about TSA, so I Googled the term. (I couldn't remember if the "S" stood for Safety or Security). Anyways, I cam across an article from Philly talking about problems with TSA behind the scenes, and the large amounts of theft going on from luggage. What struck me is that there have been a tremendous number of complains across the country of TSA cutting off locks from luggage regardless of whether they are TSA compliant or not. Quoted one TSA employee that said it was just easier to cut the lock than unlock it. Nice.
The S in TSA stands for neither one in fact, though they allege that it's for "security". And they'd RATHER cut your lock off than actually try to get hold of someone transporting an item in full compliance with the law and airline policies. As you said, it's easier for them, and I honestly think that as an organization, they're OPPOSED to actual security measures on the part of the customer (remember, you're PAYING THEM to assault you and steal your stuff!).