Congratulations on your new puppy. You were very smart to do your research and not get a yorkie if it isn't right for you. No breed is for everyone which is why there are so many to choose from.
So far as the breeder you contacted. Without knowing who it is, I just wanted to say that most yorkie show breeders do all the necessary health testing and selectively breed for health, comformation, and temperment so I'm sure if you had carried on your conversation with the breeder that you would have found out there there was a health guarantee and found out the health history in the pedigree. I'm sorry the breeder accused you of wanting the breed its puppies, but you have to realize that a lot of people want to do just that - get their hands on a quality show dog and breed it just to make money - even if it has been sold with limited registration. So the breeder was just trying to be really careful. There must have been something in your e-mail that worried them...probably asking why they were so much with limited registration. All reputable breeders sell their non-show quality pups to homes with limited registration because they aren't meant to be shown or bred. $3000 is a lot for a non-show quality dog but some show breeders charge that much and some are much lower. Anyway, just wanted to say that almost all show breeder's puppies do come with a healthy background and a health guarantee.
I know you'll enjoy your new puppy
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~Magnifique Yorkies~
Purchasing from backyard breeders, pet shops, and puppymills perpetuates the suffering of other dogs.
Educate yourself and buy from reputable breeders or rescue.