Did some googling. Apparently the Justin Bailey cheat code, which lets you play as Zero Suit Samus, was described in many publications as "it turns Samus from a cyborg into a woman". It seems people couldn't wrap their heads around Samus being a woman the whole time, and didn't know what to make of the ending even if they got to see it. Some things never change, I guess. My googling suggests that this confusion was still prominent when Metroid 2 was released in 92 but was mostly dealt with by the time Super Metroid was released in 94