Revolting subject I know but my 6 month old female kittens who were from the same litter are fed identically but one produces the most smelly poo while the other's doesn't smell at all. Any ideas why?

Different animals even from the same litters will digest food differently. Molliepops (dog) is the only one of her litter to be gluten sensitive and produce vile smelling poops, all the others were fine.

Perhaps the gut fauna is different, i.e. the bacteria and virus compositions, are significantly different. You could seek the advice of your vet and see if they recommend any of the probiotics for cats that are out there.