My opinion on the subject:
A simple concept behind Ghost In The Shell, (the anime in particular, given that the comic is much more childish in both tone and plot):
The colour of The Major's skin is irrelevant. 'Her' nationality is irrelevant. 'Her' sex is irrelevant. Kusanagi is a wholly ambiguous character. We refer to Kusanagi as 'her', because they possess a female humanoid cyborg body. HOWEVER, there are numerous story lines and threads that allude to Major Kusanagi actually being a man originally.
The whole point of Kusanagi as a character, is that he/she has transcended the need to be defined by their appearance, or who people perceive them to be. They simply do not care. Kusanagi is Japanese in name alone in the wider scope of things. They're a character that isn't bound to normal categorization or genderization.
They weren't born looking like the Major's cyborg body, as presented in the anime or manga. They were someone else originally, but they associate with the body they've chosen, because they like the way it looks.
The whole point of Ghost In The Shell is that our outwards apperances are meaningless and could come to mean even less, if we did not keep our original bodies. Sex, creed and race are all irrelevant in the eye of an artificial existence.