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

This is indeed an interesting issue, now here re my reasoning. Firstly, Luffy chose Strawhat Pirates to be his 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 Strawhat Pirates (which was 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 think of!