There are two specific and one general reasons why they didn't suspect Miss Emily. Specific reason one: they thought Homer had jilted her and left. Specific reason two: she seems to have been in mourning after he disappeared, like she was heartbroken. In fact, she seemed so upset that the townspeople thought she might kill herself. The general reason? A good Southern woman wouldn't do such a thing. In all of these cases, the underlying reason is that had another belief blocking them from considering the possibility that Miss Emily might actually have killed Homer and that's why he disappeared.
Emily's burdening presence in the town made her a societal nuisance. Homer was also a burdening presence and he was also a social outcast.
Therefore, they existed near society, but they were not a part of it. If you are not "in society" you are a nobody. Hence, she was really not someone people would need nor want to keep an eye on.
I also agree w/the previous response of her having already a history and the social idea of "the innocent woman".