There needs to be an ingame mechanism so that stealing and selling the loot is not the path to easy guilt free money. There shold be repurcussions for stealing. To make it game worthy:
1. Merchants should always know if you steal from them if you try to sell the item back.
2. Merchants should not buy any of the same items as what you stole (steal a dagger, all daggers will be suspect)
3. Merchants in other towns or shops may or may not be able to reconginize stolen loot.
4. Some merchants will buy stolen loot but at greatly reduced prices
5. You can make amends with a merchant through some mechanism in the game.
6. Fences will be availible to sell to, but while at reduced prices, not as low as the shady merchants.
7. The honest merchants may or may not do business with you if they know you stole from another merchant, until you make amends or gain trust somehow. They would not know this if you did not try to pass off stolen loot to them.
8. Your security, sneak and mercantile skills can have an effect on whether some or all merchants will buy the stolen loot. Say they think it is stolen, but you can sweet talk them into buying it.
This way you have merchants that are honest and some that are not. You can steal things if you can get away with it, but you will have a harder time selling the stuff later on, but not impossible. The threshold for recognizing or reacting to stolen loot could be set by the merchants security skill