There are a great number of anime and manga with incestuous overtones, but contrary to what might seem obvious, I’m not so sure how much of it truly has to do with a desire to have sex with siblings, real or imaginary. There are other qualities to take into consideration, such as what goes into a “little sister” or a “big sister” as a character archetype beyond simply a familial relationship, or the fact that these archetypes exist at all.
To what extent does the anime/manga aesthetic itself, as well as the other tropes that these works tend to carry, make “anime incest” into something even more different from simply its portrayal in fiction, positive or negative?
HBO’s Game of Thrones is a non-Japanese property which features very prominently an incestuous relationship. Jamie Lannister and his sister Cersei are madly in love with each other, and have even bore children as a result. However, I don’t think Cersei is thought of in the same vein as the sisters of My Little Sister Can’t Be This Cute or The Irregular at Magic High School, and therefore does not possess the aspects which make those characters so popular. There’s something to this “positive portrayal of incestuous relationships” in anime and manga that transcends the characters being connected by blood… or not, in the case of the “non-blood-related sibling” trope that technically removes the moral and biological issues to an extent.
My Big Sister Can’t Be This Vindictive
Put a different way, if the sisters, hot moms, or other family members were not portrayed visually and narratively through anime and manga, would the fans of these characters still be fans of them? If so, would it be for the same reason? My feeling is that the answer would be “no,” because it’s these incestuous character archetypes exist within a greater realm of tropes that anime and manga fans are drawn towards.
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OGIUE MANIAX 
How can you have an anime or manga of a character that isn’t visually portrayed by said anime or manga? Isn’t it impossible? And if they didn’t exist narratively, how would they (or anything else for that matter) exist? As a part of the setting I guess?
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You can have, for example, a live-action adaptation of a manga or anime property.
And there are definitely cultural assumptions that inform the writing and aesthetic execution of anime and manga specifically. For example, another case of a popular fictional incest couple is Pietro and Wanda Maximoff. But their relationship within the comics carry different connotations from how a manga might portray them, much less compared to how they were portrayed in live action in Age of Ultron. And fans of the characters tend to be fans of a specific portrayal, and not so much fans of their other versions.
Reviews of the Nodame Cantabile Jdrama have often pointed this out phenomenon, that the slapstick dynamic between Chiaki and Nodame picks up some tonal weirdness when the comedic violence is committed by flesh and blood, rather than in animated or print form. Mixed media films like Who Killed Roger Rabbit and Space Jam have also wrestled with that tension.
One field where “incest” is fairly popular in live-action is in Korean dramas: http://www.dramabeans.com/2017/06/dramaland-catnip-sibling-love-and-fauxcest/
But in most all of those examples, the actual relationship dynamic between the two parties involved still tends to be more equal than the desired animanga incest dynamic. The “nurturing onii-san” characters do exist, but aren’t with incest. Imouto characters become, narratively, surrogate daughters to the main couple, rather than a love candidate for the protagonist. In Kdramas, the same ingredients fuel different fantasies from in animanga.
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