I agree with Tracy, you need to find another vet, I have never heard of that and I have worked for a Vet for 20+ years. Zoey is my little 5 year old Chihuahua and she has an open Fontanel (Molera) which is pretty much 'normal' in chihuahuas, some close but a good majority of them do not. Zoey's is about the size of a quarter. She also has hydrocephalus (Which is NOT related to the open fontanel) her open fontanel actually is saving her life because she has excess pressure, so it relieves it, Zoey doesn't have an aggressive bone in her body...except if the cats sit on her and even then she just warns. I would look for another vet who is better versed in up to date things and has a lot of experience with chihuahuas.
Here is some information on it:
http://www.chihuahuaclubofamerica.com/molera.htm