You are caught between a rock and a hard place...I understand you can choose any pup, when they are older and not docked or you can choose your pup now at 5 days old and have it docked now but it is your pup since it's docked...hmmmm...well, I like mine docked...I would go choose and do my best to go with my gut feeling. Every Yorkie is special and wonderful and I am sure you will love your baby once he is home.
I also agree it is too early for her to be placing pups but to each his/her own...
If you feel uncomfortable and pressured, perhaps you might want to change breeders and see if due to the circumstances she will give you your deposit back. Even if she is a wonderful breeder, not everyone is for eveyone and I think you should definately feel 100% comfortable and un-pressured by your breeder...JMHO