I also believe it is not uncommon to get silkies with too few or extra toes.
I could be wrong but I really don't think it's something that can be bred out due to the nature of the gene that causes the extra toes in silkies.
It is my understanding that the gene responsible for polydactyly is rather finicky/variable in its expression. I've heard just variables in incubation (like temperature fluctuation) during development of the embryo can have an effect on the number of toes.
I've seen a few breeders mention that they'd rather too few toes than too many. Perhaps the too few is less inheritable if used for breeding?
I haven't had a lot of silkies pop up from my breeding in my own flock with incorrect number of toes. I am new to breeding and have only been hatching out of my flock since late last year though. Out of over 40 chicks hatched I think I've had 2-3 chicks with 6 toes on each foot. The rest all had the correct 5.
I've had more incorrect toes pop up from shipped eggs and I do wonder if the shipping/rough treatment might effect how many toes form sometimes.
I'm sure others more experienced than I could answer your question more thoroughly/better but in case no one else posts hopefully this might be of some use.