Technically, as zek777 said, if the cousin is at least 2 times removed from your branch, it lowers significantly risks of hereditary diseases. =/ So while it may be "incest", aside from the social stigma, there's very little biological risks.
I kinda wonder if the real reason why Uncle Ryou took Yuu Kun in his care is because he wants to sacrifice Yuu in order to properly bring back his neesan to living world (not like Haru where it's the hounds of tindalos that got stuck with Youko's appearence). I mean he looks like a desperate man who would do anything to bring his neesan back in the last page so I won't be surprised if he actually gamble on a shallow theory like "exchanging one blood/soul with a biologically related one" as long as it has the possibility to bring Youko back
just wondering, in which chapter was there anything about Yuu's mother being sick? (the sickness that everyone in this thread is talking about)
edit: nevermind, I read chapter 29 again and figured that out
So here is my speculation so far..
Uncle ryou summoned Haru(the hound of tindalos) as a replacement for her onee-chan
When Uncle ryou learned that his onee-chan died, he tried to summon another Eldritch creature(hoping it was Cthulhu), things went awry and he went insane from it, and end up summoning a lot of eldritch creature along with Chiyo(Shub Niggurath)
@Baldulf It seems most likely Yuu does not have/has never seen photos of his mother at his age/as a kid; he's only seen his mother as the fully grown woman she was & has no frame of reference to what she was when she was younger.
@Sam_Arcade: I just realized that I was confused by your use of "her" instead of "his", and somehow missed that you already did that in the sentence prior to the one that I had quoted.