When I originally introduced Samus into the Two Evil Scientists Storyline, I considered having people assume she was a guy, much like in the original Metroid. But I thought that might get a little confusing, and repetitious having every character go through the same thing every time she met someone new. Let's just assume that she upgraded the voice filter on her powersuit so that her voice doesn't sound so deep, and she lightened the tint on her visor so people can see her face better.
...meaning...she got breast implants?
the suit also becomes more form fitting in later games, but when she's not wearing it I don't think anyone would mistake her for a guy