The reasoning behind pink hair has always perplexed me. The palette reasoning has been cited for ages, but I have big doubts on that. He has plenty of colors on his sprite that could be used to make his hair a dusty brown color OR blonde, like it was in the past games and the ALTTP official art, respectively - the pink is an
extra color on his palette. His sleeves are brown and his belt is yellow, meaning the colors to make him either blond or brunet already exist. So yes, it is intentional. They went out of their way to make his hair pink.
Seeing as ALTTP Link is always portrayed as blond in artwork / canonical appearances, I have no idea why they decided on pink hair for the sprite. Do I love that he does? You bet.
Do I understand why he does? Not at all.
Maybe it makes him pop out from the backdrop or something? Did they think it made him look more mystical?