Do the shopkeepers mention the murder or know you did it? What about enemies adjusting based off skills?
One apprentice who took over a shop after I terminated the previous owner would greet me with an "after what you did ..." type of comment but, didn't have any problem selling me stuff.
It really didn't make sense though given that he should have had no way of knowing that I'd knocked off his former boss and all potential witnesses in a cave miles away from town.
Guess it's just another mystery, like the "how do shop keepers know something is stolen" question and the "sneak thief" comments from guards after you've stolen something that you weren't caught for or witnessed doing.
Maybe some people in Skyrim can read minds or I just have a guilty looking face ... who knows?