In the beginning mangaka drew their characters like Western people to make fun of the West. It was their way of slightly rebelling against the ones who forced them to open their country to the rest of the world.
Nowadays though it's a mix between Japanese and Western looking characters probably because they want to make it a bit more appealing for the Western audience. Also because Japanese people are fascinated by the different colours Western people have for hair for example. They find blond for example very interesting and special, because it isn't in their genes to have natural blond hair. Western people however can have brown hair, black hair, blond hair, red hair ...
So it's because of their slight fascination for different Western looks probably as well that not all characters have Japanese looks.