Naked neck is (semi)dominant. So any chicks with not-naked necks do not have the trait at all and will never pass it to chicks. Even if both of their parents were NN- once "it's gone, always gone".
The not-naked chicks prove that you have at least two birds that are not pure for the naked gene. This is very very common actually. Especially with backyard stock- quite a lot of people let them cross with anything and sell all naked necked birds as if they were THE breed even if they obviously have small crests or leg feathering or are otherwise obviously crosses due to color or appearence. I do see a lot of not pure for the naked neck gene in hatchery stock also though.
With single combed birds it often is possible to tell by sight which birds are pure or not pure for the naked neck by the size of the neck patch. If this patch is large and the feathers cover up the lower front of the neck, it is not pure for the gene. Pure birds have very small patch with only a few feathers and the lower neck, chest and full crop are usually extremely visible. A lot of people will claim that only the birds with totally bare necks are the ones pure for it and anything with neck feathers are not.. this is not true. Most pure birds have a very small neck patch and will throw 100% naked necked chicks.. (I have tested and bred hundreds of naked necked birds)
So if you want stock that breeds pure for the naked necks, just look at the chicks and you should see a difference in the neck fuzz size.. the ones pure for it will literally seem to have just one or two fuzz-feathers on the neck while the not-pure have a much larger fuzzy patch covering most of the lower front. Once you keep and breed the birds with very small neck patches, you are set for a pure breeding line. It's easy.
It is much trickier with birds having combs other than single. Pea comb also has the effect of reducing feather numbers on a bird, a not pure naked neck with a pea comb can be quite naked(including a small neck patch) and look like she is "pure" due to her "nekidity".