Best to listen to those episodes -- it's complicated.
No, we do it ourselves because it is much cheaper. A vet will get more accurate results, since they know how to swab properly. I had a heck of a time learning to do it right. Not sure what 'vets don't specialize in nidovirus testing' could even mean. Sounds like someone was trying to impress you, frankly.
Vets can certainly make a call that hindsight shows wasn't the best one, but proceeding as your vet is doesn't sound unreasonable. Most herp owners tend to want to keep costs down so that's the default. If you slap your credit card down and ask the vet to throw all the diagnostics at it, I would be willing to bet they'd cooperate.