Hairs turns out to be more interesting in EGS than in real life lot of times. This page aggregates the most important cases.
Mysterious hair and eye color Edit
Yes, in EGS universe, there are characters who's natural hair and eye colors don't match their genes. Examples include Nanase's red hair, Tedd's purple hair and Liz's green hair. (Also, Ellen's green hair was mentioned, but that's likely slightly different case ... just like Susan's dark blue hair she got after awakening.) Scientists noticed that but wasn't able to find out the reason, although it IS taught in biology.
It probably does have something to do with magic, but Tedd doesn't know any details.
Out-of-universe explanation, of course, is that Dan just liked such colors, and was terrible at drawing black hair at start.
Hair "spontaneously" changes color Edit
On a related note, DGB arranged for sudden hair or eye color changes to be listed as medical condition. This would be primary for cases of magic burnout, but might be used for hair changes as part of awakening as well, if it happens more often than just to Susan.
There is quite a lot of transformation spells affecting only, mostly or noticeably hair. Starting with FV5, then Nanase got disguise spell initially limited to hair. Then we have whole storyline named Hair (story line) about Tedd making watches for shortening hair, originally meant for Nanase but given to Sarah ...
Magical hair manipulation fairies Edit
As mentioned in Artistic License versus Actually Happening#Magical hair manipulation fairies, there is so much artistic license effects with hair like badass-hair-in-wind-without-wind that in Q&A continuity hair manipulation fairies actually exists. They are unlikely to exist in canon, though.