She's a girl. She's based on "Prince Shoutoku" and in Touhou context she is literally supposed to be him, but it isn't as if Touhou needs to stay completely dependent on history. Prince Shoutoku never did any superhuman feats (although saying this is ironic considering Miko was transported to Gensokyo because people stopped believing she did superhuman feats), and buddhist priests never built a temple on top of his grave.
