Maggie,
You're correct to second guess this recommendation. The shop that addressed the locking hubs may have overlooked something or created a new problem, it's very hard for me to make that determination though. If wheel bearings are bad, they will be noisy all the time, not just in 4WD.
Here is a picture of the locking hub and the bearing, you can see how they are in very close proximity to each other.
http://bit.ly/b1XU49
I suggest you get all the information about the repairs made and the suggested repairs and talk to the manager of this shop, if they are unwilling to help out, then take this to another shop and have them inspect to see what is happening.
My Opinion: This shop screwed up and is trying to cover their butt. Making mistakes is not-uncommon, however they need to accept responsibility if they messed up, and you may need to take action if they wont.
Good Luck