If their love childs' bloodline is accurate to theirs, the sister's eyes could've been either purple or red, just like their mothers.
Ignoring the fact that genetics don't usually apply to anime, blue eyes are a very recessive trait. Nico and Maki could easily have the gene without expressing it.
Blame benja. As soon as I say that post and noticed a distinct lack, I had a Misdreavus needs to Smeargle some. Given the chance, I'd Doduo it all over again.