First, I am so very sorry for your loss
Contrary to frequent belief, vaults do not necesarily create a larger crest. However vaulted skull birds do tend towards larger crests, whereas with non-vaulted skull birds you cannot tell what the size of the crest will be until the bird is much older. I will say that your photo shows a very large vault. Most silkie breeders that I know do not select for or against vaults--a few years ago some breeders did, but I do not think that is the case any longer--at least for most. Unlike polish, the standard does not require a vault.
Yes, vaults can cause problems, but I have to say I would suspect something else in brand new hatchilings. Check the temperature, the feed, any bedding present, the water. Did the ones who died have any amount of pasty bottom? Is the waterer one made for bantam chicks--also called a quail waterer--or filled with marbles to prevent drowning? Might they be eating the bedding? Is the food smal enough for them to eat (although they shouldn;t need any for 2-3 days)?
Check those who are left to see if there are any mites/lice. While an adult bird can go days or even weeks before the bugs will kill them, they can kill chicks in just a day or two. Look under their wings and use a magnifying glass and bright light--watch for anything moving at all.
To your unstated question about why not all the eggs hatched out splash, both parents would have to be splash to guarantee splash offspring. It is thought that splashXsplash will eventually wipe out/reduce the splashing, so many breeders mix blue, black & splash together. I don't hatch enough for my experiences to have any statistical bearing, but my splash X blue pairing that resulted in my first splash pullet who was far paler with far fewer splashes than my current splashXsplash offspring, who have as many splashes and colour contrast as could be wished for. Now if I kept on with this through several generations, it might well dilute the colour to near white with few splashes.