They came in through a bedroom window (presumably on the second floor). The shots were in the basement. It is conceivable that the sound was sufficiently muffled by distance and intervening ceilings that it didn't register to her that they were shots.
Nonsense. A gun goes off in the basement the whole house rings.
I notice from the article update that the police are still investigating the crime scene.
They thus far are only saying that the two broke and entered and were burglarizing the home.
I’m sure they are looking carefully at his story of shooting them as they were coming down the stairs to the basement.