I just did a bit of poking around at various sites to find the background of the historical Amakusa Shiro(u) Tokisada upon which the SNK character is very loosely based, and it seems that this person was male. I also saw a couple of other Shiro-inspired fictional characters, and both were male; the only thing I can think of to explain the ambiguity would be that the SNK character seems to be undead, or in some other "humanity"-altering state (he seems to be capable of transcending ordinary physical existence, at least temporarily) that might have an effect of making the person androgynous. Of course, I came up with this theory in all of about 3 minutes of thinking lightly about it, so I can't imagine that I'm actually right <IMG SRC="smilies/biggrin.gif" border="0"> .
As for plot, I'm fairly uncertain about that, but I think it has something to do with Amakusa being raised from the dead (or otherwise transcending the life/death barrier) by his hatred of the Tokugawa clan and generally acting as a conduit for evil to infect the world. I could well be mistaken, but I get the impression that Amakusa doesn't actively spread evil; evil just kind of tags along and makes things suck whenever he's around, thus making him a target for righteous slashing. Or something. <IMG SRC="smilies/loco.gif" border="0">
I think I need to go to bed.