The "she" title is only present because it is a version of Samus who is obvioulsy female. In reality what genetic code Metroid Prime took to respawn into Dark Samus doesn't really mean that Prime will be female in the Dark Samus form. I'm not saying that Dark Samus is male either. What I'm saying is that Dark Samus has no gender because it needs no gender and like I said, they refer to her as "she" because Dark Samus is a representation of Samus herself.