My hamster is a carnivore...

Well there could be a lot reasons why they are missing. Have you checked the area where she gave birth? They could have fell off the cage or something. maybe you counted them wrong. Anyway, its very normal for hamster to eat their young, specially if its a first time mother. Avoid touching the pups until its 2 weeks old or else they will surely get rejected by their mother and normally just eats them. Also, provide as much food as you can for the hamster will secure herself before her pups, if she gets hungry and no food is provided, she'll definitely eat her young.