I used to be a vet tech for years and where I live that vet office would probably not last long. I believe sanitation is part of the law, especially sharing the poo on the thermometer!! Here a thermometer has to either have disposable sheaths, which ar changed after each dog, or they have several which have to be soaked in a disinfecting solution after each dog. I am pretty darn sure the tech was breaking the law.
As far as the cleanliness of the office, if smell was the only issue, that could be explained by having a very stinky emergency that cause it before the clinic opened, however, if the place LOOKED unclean, then someone wasn't doing their job. Cleanliness is so very important (germs, parvo, etc) and a vet MUST be aware of that so by having a dirty clinic they are telling you right there that they could care less about the welfare of their clients animals.
The receptionist was just plain ignorant. I get these kinds of comments whenever I take Alastor out. He is pretty much always in his stroller, purse or just being held. the little guy is only 2 1/2lbs, so there is no way I am having him walk around people who could step on him etc. besides, he LIKES being off the ground. The receptionist may or may not be a reflection on the clinic, in this case I think she surly is.
The vet is pathetic, IMO. There are several around here who seem to think that we pet owners should bow down to their all knowing expertise of all things animal.

Does it really matter if the vet truly does "know" something we do not about vaccinations etc. Their job, as well as taking care of our pets, is to help educate us, the pet owners, as to how best take care of our pets, and to answer all our questions respectfully. I have a feeling he probably washed over your questions because he was most likely intimidated by your interest and didn't even know the answers to your questions or even understand the issues.
You did the right thing by protecting your pups. Who knows if they even refrigerate the vaccinations properly, use expired vaccinations etc. Because of the obvious lack of care they show elseware. I certainly would NOT be suprized.
Perhaps you can write a letter to the editor if reporting them fails, so at least other pet owners will be warned.