User blog comment:AYET/Pirate Crew's Jolly Roger/@comment-3425840-20120312081656

This is indeed an interesting issue, now here are my reasoning. Firstly, Luffy chose Strawhat Pirates to be his crew's name as he treasures his hat and thus cares more about it than the scar under his left(!) eye.

Now to the main issue (that is why not  Three-scars-at-left-eye-left-by-the-bastard-Kurohige  but  Red Hair ), I think that when Shanks settled for his Joly Roger he still use to have the possession of his trademark Strawhat. Now normally he would wear the hat and thus his hair would have been covered. As naming them (the Red Hair Pirates) the Strawhat Pirates (which would have been the normal course of action) would disrupt the plot for Luffy in the future, Oda had to settle for Shanks' secondary trait which could be noticed easily, the scars. Basically, the  "since hair is covered by hat I will go with the scars"  policy. Well that is the only reason I can think of!