Kobeni will suffer some sort of more serious consequence as the result of her having absorbed Youkai energy from Hakuya.It was stated that the reason Kobeni is often an Ill Girl is that Hakuya had to give her his energy in order for her to survive when she was injured. There is the potential that later on in the series Kobeni will have a severe health problem as a result of this and have to be saved, perhaps with some sort of ritual cleansing. She might even get possessed or die, but that seems very unlikely due to the light hearted nature of the show. Alternatively...
Kobeni's health will improve for some reason and she will no longer be an Ill Girl.Perhaps she will remain about the same throughout the series but some event will end up curing her and allowing her to enjoy her life more.
Kobeni having been given half of Hakuya's energy has transformed her into a half-Youkai and will give her special abilities at some point, possibly after she is made healthier.
Hakuya's hair is hiding a scar.Like Kobeni, he go hurt in the accident, and the way they said it sugested it was quite serious; she got a scar in her side, his was in the eye.
The Mitsumine Family is actually the Koshigaya Family from Non Non Biyori.Extending this WMG from Non Non Biyori, the Koshigayas turned into the Mitsumines when Natsumi wished that her mom and her sister would get off her case, and her brother would be more assertive and get a girlfriend. Unfortunately for Natsumi, this wish was granted at the cost of her life, and her family's humanity.
The Yonomori Family are also YoukaiThere's no other reason to knowingly allow humans to interact, let alone marrying with, youkai. The family name does not help; it literally means "forest-at-night." The siblings' names would be red things at such situation... not exactly a good sign.