Sorry, I just can't see this happening...
The luggage handlers do not know what is in your bag, only the security at the main gate where it is x-ray'd do and since that happens with you there (for the most part) you would have seen them do it
Also, the luggage handlers are extremely busy and I can't see them rifling through random bags to go for pins.
Pins have no value (I'm not talking sentimental value of course...just $$$) so why would anyone want them as opposed to the millions of actual valuable things that would be in peoples luggage (if you're gonna steal...it's not going to be pins)
Also, this would mean the luggage handler KNEW there was a bag coming with pins he/she wanted and showed up to work with pins they wanted to trade.
Not a likely situation. I would check with your kids to see if they remember all their trades because the way people trade pins sometimes you can get caught up and realize you traded one of your favorites.
Maybe on their next trip they can keep an eye out for their favorites and when they get them, tuck them away instead of keeping them on their lanyards where they may get traded accidentally