If I steal from a shopkeeper, are there any consequences to being able to buy or sell form them later? Like, if I steal alchemy ingredients, will they permanently be out of stock on them?

Anything else I should know?

No nothing to worry about as far as I know. Have stolen everything from several shops and have never had anything happen.

I have found no consequences yet. I robbed all the alchemy shops and when I came back after a quest or two they were all re-filled. I think they stock up quite
fast.

Nice. I think I remember in Oblivion that if you stole something, it was gone forever. I might be wrong though.

I stealed from belethor and he seended Thugs after me.So yes....but i was smarter and used fury on them.So all the town start to kill them and them kill themselves xD

Hahaha awesome! Did he know you stole from him because you got caught, or did he just know?