Kappa are traditionally depicted as having turtle-like aspects, including beak-like mouths and shells on their backs. Nitori's backpack is sort of a stand-in for the more usual back-shell. Since Yachie and Genji have actual turtle shells on their backs, Nitori's "completing the look" of a kappa, from her perspective, by giving them matching caps and, in Yachie's case, a matching backpack.
Kappa are traditionally depicted as having turtle-like aspects, including beak-like mouths and shells on their backs. Nitori's backpack is sort of a stand-in for the more usual back-shell. Since Yachie and Genji have actual turtle shells on their backs, Nitori's "completing the look" of a kappa, from her perspective, by giving them matching caps and, in Yachie's case, a matching backpack.
That was informative. As for Nitori, she should have made cutouts for Yachie.