Actually, the size of BOTH parents and the other dogs within their lineage play a role in the size of the pups. I would have asked your vet how many litters of Yorkies he/she has delivered as he/she obviously felt that his/her knowledge was more accurate than that of many long time breeders. Then I would have found a new vet. You did your research and decided on what YOU felt was the best option only to have your vet deny your requests?
All you can do at this point is prepare the best you can, which is sounds like you have done. Have an x-ray done when she is at the 50 day mark. This will give you a guessitmate on how many pups to expect and more importantly will give you advanced notice if any of the pups look too big for her to deliver on her own. Try to find an experienced breeder local to you who would be willing to come and assist you during her whelp.
Good luck and keep us updated.