I think the bits and pieces are just obscured because the show was created for television. In the picture, there's really not any detail either way, and rightly so as depicting anything of that nature would be inappropriate on a child. Most everything I've seen points to Shippo being a little boy. To support this, in episode 55 he develops a crush on a young girl with a "jewel shard".
I think of it along the same lines as a Ken doll... he's hardly anatomically correct either. Imagine the stink mothers everywhere would create if Mattel corrected that issue.