Vaulted skull almost certainly has a genetic cause, but I don't think anyone has figured out how the genetics work.
To avoid it-- buy from a breeder, and specifically ask for ones that do not have vaulted skulls. (Feel the head with a finger, and compare with non-crested skull shape.) If the breeder only has vaulted skulls, look for another breeder.
Or buy from someone on backyardchickens, or on craigslist: any way that you can examine the birds before purchase, and only get the ones you want.
Hatchery birds--might have it, might not. Might be different from one hatchery or a different hatchery. If the chicks from a hatchery are for sale in a store, you could check for vaulted skulls if the employees will let you.
If you order birds from a hatchery, you could choose to order extra, check when they arrive, and cull any with vaulted skulls. But you will not know until they arrive whether all, none, or some will have vaulted skulls.