Maybe not.
[link|http://arthistory.about.com/cs/last_supper/f/john_v_mary.htm|About.com].
Remember that comparison of Leonardo's self-portrait and Mona Lisa? [link|http://www.lillian.com/|Mona Leo]. While Mona Lisa is in all probability a portrait of a woman, he clearly could introduce some doubt to modern eyes.
Leonardo feminised a lot of his subjects. He also played with the ages of his subjects - I think it was common in the time. E.g. Michelangelo's [link|http://en.wikipedia.org/wiki/Piet%C3%A0_(Michelangelo)|Piet\ufffd] shows Mary as a looking like a 19 year old girl.
The [link|http://en.wikipedia.org/wiki/The_Last_Supper_%28Leonardo%29#Composition_and_meaning|Wikipedia] article on it is pretty convincing, IMO.
FWIW.
Cheers,
Scott.