For the las few days I have noticed that the characters from Whiterun that run the Smithing shop are not there anymore. They seem to have disappeared, the woman outside working is not there and the shop keeper too. The doors are locked all day long. I am really sure that I did not kill them at any time during my playthrough. Can someone tell me why this has happened?

You scared the hell out of them. That'll teach you to bring in werewolves in Breezehome.

Try to break in and see if theyre somehow stuck somewhere, who knows? Maybe they killed eachother lol