1. The entities in the warp seem to be entangled with (mainly) human emotion, the warp is us... however we mainly see negative manifestations, where are all the positive emotions? I understand that Khorne also stands for courage and brotherhood, the clean kill and all, and Nurgle has a certain 'fatherly' feel to it, still, where are the positive emotions (in ToH there was one positive example).
I would surmise that the creatures born of negative emotions would eat the ones born of positive emotions, if there are any to begin with. Rage, Lust, Fear of Death and Ambition are much stronger feelings than say Love, Happiness, Compassion and Humility. Creatures born of the latter and only able to experience the latter would find it very hard to function, whereas the former find it much easier.
2. A projection on the 40K setting, this would mean the warp would never let nids and necrons slay mankind as it would mean the end of human emotions, also the gods cannot afford to be not interested in humans?
Likely not. I am reminded of what Nagash says in the first of Mike Lee's trilogy, something along the lines of "The Gods should take their goats and be grateful, they need us far more than we need them." The same thought applies here, the Chaos Gods are our darker emotions given form, and if their connection to us is as strong as Khayon believes it to be; then I think that yes, they need us to continue existing. Without humanity, Chaos would wither into nothing.
3. Horus versus Abaddon + marines, I would say the Horus clone is only a meat clone without his strong aura in the warp, as Betrayer learned that marines are genetically bred to be in awe in the presence of a primarch, this cleary not being the case. Plus Abaddon seems to be physically the equal to a primarch making it very strange to believe a BA chaplain wounds him.
I think he was the real deal, the awe was absent because they were being assaulted by him and in my opinion because the entire group had internalized their distaste for the Primarchs and that was enough to overcome the trans-human awe that the Primarchs invoke in all who see them. As for Abaddon and Jorus, we'll have to wait and see, but I agree that Abaddon here was terrifying, but I think that if Jorus did manage to wound Abaddon so badly that he still has the scars by 999.M41, then he must have been a Badass among Badasses. (I mean, he did manage to wage a guerilla warfare campaign using the psychotic Death Company and kept them all sane while doing it, on his own.)