Ok so I'm trying to see if I can steal some of the unique items for sale at shops (i.e. Hands of the Atronach at the Mystic Emporium), but I'm not finding them while sneaking around at night. Do the owners equip them at night and sleep with them? I've heard specifically that Hands of the Atronach can be stolen, but not where they're hiding.

I suspect you heard wrong. A shopkeeper's inventory is not on his person so you can't pickpocket it. It is not in a chest or container in his shop that you can access in the game via normal/intended means. It is kept in a special manner that is designed to be inaccessible by players. I am not aware if there is any glitch to bypass this without using the PC command console. Regardless, there is no challenge to your thieving skills available here.