Regarding gender.
None of this is canon for Nabari no Ou. This is my own head canon and personal research.
As Yoite is an intersexed youth and it's not quite detailed as to what kind of disorder he was born with, I took it upon myself to answer that question, because. Well, he's not exactly a sexual kind of person, but in case the question comes up, HEY, I won't be floundering aimlessly. Better to know these things.
This is all information Yoite himself isn't even aware of, as he doesn't recall the name of his own disorder and he doesn't really WANT to know. It disgusts him, and he refuses to learn more on the subject. He just wants to pretend it doesn't exist.
My version of Yoite has something called 5-Alpha-Reductase Deficiency (5-ARD), which is a recessive condition resulting in the body's inability to convert testosterone into dihydrotestosterone (DHT). Because DHT is required for external genital growth in the womb, genetic males are born with ambiguous genitalia. If you would like to read more about the condition, there is a very good, detailed article [here] - just beware a lot of difficult-to-read medical jargon!
This means that, while he is technically a male, he does not have traditionally male genitalia. Yes, this Yoite has a vagina. It's slimmer than that of a normal female's, as it's underdeveloped, and he doesn't have the working parts of a normal female - absent uterus and fallopian tubes. However, Yoite also has a penis. It's fully functional, but infertile; also, much smaller than average, at two inches.
His testes are internal. Yes, he has a hymen. Yes, he has a clitoris. Yes, he has a prostate.
TMI! I know! But I just know the question's going to come up at some point. Figured I'd answer it as in-detail as I could.
Should anyone have any more questions, don't feel afraid to ask!