Our Humane Society will separate feral litters as soon as practical. If left together, the feral behavior in one can amplify the same behavior in others. With that said, each litter is assessed individually. One litter we took on last year had 3 kittens - 2 were more human friendly and they were fostered together. The wild one was separated and put in a foster home where all the cats were non-feral origin. They are then adopted out once they have been socialized. In the case of this litter, all 3 were adopted to separate homes and all 3 turned out fine, even though 2 were in the same foster home for about 4 months.
I've brought in a number of feral litters over the years. Of all of them, I have only adopted a pair together once, and those were orphaned at 10 days old therefore were highly socialized. I have kept feral pairs (Tigger and Eightball, Pinky and Ruby, Morrison and Hendrix, Muddy and Koko) with success. Only Tigger and Eightball show the very scared signs of being feral, and interestingly, they are the pair that didn't hang out together in my house. So their feral behavior is simply part of who they are, not based on the fact that they live together.
I'd recommend separation if they are extremely wild, but allow them together if somewhat tame.