Funny that this should come up... I was in the local pet shop today helping a client buy the appropriate supplies for her hatchling, which she picked up from me at the same time. Afterwards the owner approached me about being a possible supplier. Obviously things will vary from shop to shop, but his intention is to sell reptiles for roughly the going rate. He may charge $50 more than a breeder, but he is not going to pay breeders full price because he has to wear the overhead, permit costs, etc. His prices for gear are not too much more than online and he stocks a great selection, which is why I had a client there in the first place. I might sell a few animals through him, as I am convinced that he will have a reasonable setup (most animals will not be on display) and has enough herp experience to give good advice to customers as well as to care properly for the animals. He will be selling reptiles that he breeds, so he has a vested interest in doing it right.
I don't think that most good pet stores will sell outrageously expensive animals because it is easy to find out how much a reptile SHOULD cost. Then again, look at the prices for mongrel puppies in shopping malls...