Pokemon seems to be ambiguous about its hairstyles. Remember the male trainer from Ruby/Sapphire? Is his hair actually white, or does he just have a bag on his head?
The Pokemon Special manga isn't "official", you know. Technically, Ruby is a completely different character from Brendan/Yuuki.
Haven't you ever heard of artistic license?
If you squint at the official Sugimori art of Yuuki, you can see that the sideburns are the same color as his hat/the rest of his hair. I prefer to think of it as his hair, but if you want it to be a weird-ass hat, it can certainly be a weird-ass hat.
As for Natane, I always thought it was just the part of her hair that was cast with shadow, but this is a cute idea.