What? Last time I tried it out of curiosity I just casually emptied a merchants entire inventory without any trouble. Did they change something with the recent patches?
The problem is that you can just save scum to empty all merchants of their stuff anyway. DC's are pretty low, add in some Guidance and just take whatever you want.
The only way I see stealing becoming a balanced mechanic is either...
a) Severely limit what you can steal. Merchants should secure their valuable stuff better. Have stealing have a lower impact overall. Or...
b) Create some kind of reputation mechanic where even successful thieving eventually gains you a reputation as a notorious thief. So even if you don't get caught, there would still be some consequences for getting all that stuff for free. Merchants everywhere would stop trading with you in a normal fashion or offer bad prices. If you want to steal stuff without getting a negative reputation, wait for night time, sneak into stores and make sure there is no one anywhere.
Oh right, BG3 thieves only steal in broad daylight.