I like when hospitals are AAHA accredited. It shows me that they meet minimal standards as far as their business goes. There are a ton of bad AAHA vets though. They are not obligated to use the same protocols that AAHA stands behind or anything. I've seen a couple really bad AAHA vet offices. While I'd have to wonder why an office isn't accredited and it would bother me, I also would not make this part of my decision when choosing a vet. I'm thinking of three AAHA accredited vet offices right now where the owners would not be touching my dog - ever. Bedside manner isn't hte only problem in these cases either.
Bedside manner, though, is a very large deciding factor in choosing a vet for me. Unless it's a really good specialist and I only have to deal with them a few times, I want somebody who has an amazing personality. I don't like dealing with people who aren't interested in being kind and non-condescending.
Maximo, you could just ask why they aren't AAHA. They may tell you.
Go with the vet you are really comfortable with. Good vets will work with you on a vaccine schedule and not make you feel guilty for not doing it annually b/c they care about their clients' feelings.