Yes, these companies won't guarantee their vaccines unless properly administered, but they are still sold to the pet owners directly. I believe rabies is the only vaccine that must be administered by a veterinarian.
You're right that most vet clinics aren't depending on those cheaper meds. But when we get into heartworm and flea prevention, the ability to get these prescriptions online is a serious threat to vet clinics. Those prescriptions are pretty decent chunks of income for the clinics I've worked at. A year of large Heartgard hovers around $100 per dog in my area. Multiply that by 100+ dogs we see on that dose....you see where I'm going. If that revenue is lost, you're sunk. Vaccines and heartworm/flea prevention are now available online. Part of this was due to the actions of veterinarians with personal interests, which is why the new flea preventions that are coming out have tracers on the packaging. I think that might help the problem, but where there's a will, there's a way (see the Frontline Plus disaster).
As for generics, they are often tested less frequently/rigorously when compared to name brands (this goes for human medicine too), allowing more frequent changes in purity and inactive ingredients. Actually, generics aren't tested at all sometimes. As long as the potency of the active drug is the same at the initial request to manufacture, they can bypass the testing periods the name brand went through and sell their generic with the same drug, but different inactive ingredients (sounds like it shouldn't be allowed....but what do I know). I'm not saying that you're going to kill your dog if you give it a generic (often that's all some vets carry) or that drug companies are producing placebos and selling them as active drugs, but it's something to think about.