JLP603

I'm not sure it really applies to Koiken Otome, but...

Akatsuki no Goei, though it is mostly humorous and/or fails.

Jesus Christ, just read Lolita instead

anyone know japanese visual novels, translated or untranslated with this kinda ending: Specifically you get a girl pregnant in one of the heroine's routes -> you then timeskip and have sex with her and your daughter.
so far I found these after combing through vndb: shoujo dominance my precious reina (in one ending the protag has sex with his daughter and his grand daughters after getting the daughter pregnant), iyashinbo the animation (harem end where seemingly based on the cgs the daughters of the heroines and they themselves have an orgy with the protag), Chichi Miko!! Plus 1 ~Sobo to Musume no Sakunyuu Harem~ (in a sense that the main heroine is the daughter of the protag and a heroine from the prequel),
Kimi dake no Botedol! ~Hakudaku Mamire no Tenshi~ (the unlockable heroine is the daughter of the main heroine and the protag) , Junketsu★Megami-sama! "Tanezuke Shite Kudasai, Danna-sama!" (where the game lets you have sex with the daughters of you and the heroines using the phone near the end of the game), Kikenbi Neratte!? Haramase Gakuen 1& 2, Kouki na Ojou-sama o Katappashi kara Haramasetara, Dou Naru ka?, (cg shows protag having group sex with heroines and daughters), and まままままま (where in the cgs it seems some routes the protag has group sex with the heroine and their daughter)
Let me know if there are any other sites I could be asking this. I'm all ears

Nice. Thnx for the recommendation!

Ayumi's route in YU-NO addresses it. (https://vndb.org/v1377)

If you mean "address" in the sense that the taboo aspect is emphasized and side-characters being kinda creeped out:
Natsuzora no Perseus (JP only) https://vndb.org/v10597
 

Most Minori games?  They always have twisted incest routes in Minori games that are as much about people's reactions as they are the relationship itself.  Just look on vndb for any Minori game with the incest tag or a sister heroine.
To a more comical extent, any Clochette game with a little sister has an incest route, usually with the little sister being an obsessive brocon who doesn't understand propriety... there usually aren't any huge obstacles to the relationship though, since most people around them are usually aware of the sister's feelings and are at least reluctantly supportive.
Soshite Hatsukoi ga Imouto ni Naru has a lot of messed up characters and two 'imouto' paths, both of which have their own issues that are pretty serious.  Honestly, this is one of my major recommendations for imouto routes in general.
World Election has a decent imouto route, but it is similar to Clochette games in that there aren't any huge obstacles.
Yorite Konoha wa Kurenai ni has an imouto route that isn't my favorite, but it does deal with those issues to an extent.
Unmei Yohou o Shirase Shimasu has a seriously, badly twisted imouto route that deals with the issues you mentioned, along with a lot of psychological trauma and the protagonist having been a total a-hole as a kid.
Reminiscence has the single best sister route ever, and while there aren't any social issues involved, there are a ton of hidden issues between those two that are pretty messed up and horrifying.
Kanojo-tachi no Ryuugi is another one with pretty heavy-handed imouto routes, though the reasons are pretty evident early on.
Real Imouto ga Iru Ooizumi-kun no Baai
Koiiro Soramoyou
Tayutama (the original, not the localized one)
Yome Sagashi ga Hakadorisugite Yabai!  is another good choice, though this one again is less about social issues than adjustment issues.  (really, any of the Yabai! series will work, since the imoutos are all brocon heroines that have a lot of internal hangups)