Ahh. I'm seeing how odd your situation is.
Honestly man, without knowing for sure, it's tough to really point the finger at the man who takes care of your vehicle. It would strike me as odd if he were to do something like that anyway given that it's 1. such a minor thing and 2. doing so would basically be suicide for business over a $40 piece. I know the media likes to make a big deal about scams and what all have you, but seriously, any reputable shop won't be pulling shit like that. It's exceedingly rare. Brain farts while working? Getting a hold of ****** parts you don't know until after the customer leaves? Common. If he said he didn't have it - i.e. forgot to put it back on, I'd believe him. Otherwise it's just taking up shelf space until he deals with it. If you truly believe this is an issue, you can call your bank and have it formally investigated, you can also check reviews on google/yelp/FB. Should your mechanic have sticky fingers, it's unlikely that you'd be the only one affected
Given the peculiarities of your situation, I think it would be worth your time to up the security on your vehicle a little bit. Viper has some smart alarms that sync with your phone. And since a hood latch is just a pull-cable, they're quite easy to relocate to somewhere else. At the end of the day, anyone can take anything they want, but you don't have to make it easy for 'em.
Spitballing other ideas:
Structural laminate over the windows. Even if they break, you still need to do some work to get the stuff off. Not a good idea if you drive over water for obvious reasons.
Plate or block of wood, something along those lines to protect the hood latch so it can't be "fished"
Some sort of lip around the doors so it's more difficult to poke a coat hangar through and press the latch
Kydex or some other sort of plastic cover over the door internals. if memory serves, these vehicles use the old school systems that can be unlocked from going between the window and the door.
Consider a battery backup for any sort of car alarm. Wouldn't be difficult to rig up with some diodes
Shave the exterior door locks. Understand the risks if you do so, however.