Even I can not stand the genre Loli (perhaps because I'm a father, but Oni Chichi disturbs me) and in general father/mother with sons are a bit difficult to accept for me, even when the situations are amusing or bizarre and seem more acceptable.
But, indeed, most of the times the incestuous relationship is apparent and not real.
So, for example, in Nageki no Kenkou Yuuryouji, where Hiroe calls Mayaka Onee-chan (sister) and Yayoi Okaa-san (mother). To adapt to the sensitivity of a Western audience and not to represent the relationship between the three as incestuous, the translators of the american version have added various notes to explain that the women are just housemates and the landlady, even if an anime fan knows that Onee-san and Okaa-san can be mere honorary titles used for respect. (By the way, Nageki is a my multilingual sub, as Kitsune, but unfortunately not in German. It existed but I could not find it and if anyone knows where...)
Often then, in the hentais the relationship is less strict: the incest is between cousins (see Nee Summer) or acquired brothers (Ane Yome Quartet) and mothers, who therefore have less or no blood ties, and more rarely between real siblings (Cleavage and Aki Sora, although this second is extraordinary in many ways).
Perhaps the true question is what incest is and to what extent it is considered acceptable in Japanese culture.