Responses
I believe Shoui figured it out himself eventually..and look at this page where Waki says, you're exactly like your father. http://www.mangago.me/read-manga/ze/an/mi_chapter-40/pg-9/
The look on Shoui's face (on the next page) his eyes, tells me that he knows who his real father is. He's a sharp guy.
I seriously love this manga! When I first read it, I initially didn't like it because it was so strange but the more I read, the more I came to love it :) The only question I have is if Shoui knew he was adopted since Sensei never mentioned it. If females lose their power after giving birth, it makes sense that Shoui realized the truth but I guess it's up the the reader on that aspect