It’s an interesting theme of course, and as such worth exploration. I would not disparage the idea of the incomprehensible extraterrestrial. And, it has been very well done. Lem’s Solaris, for example, is a masterwork of the subgenre. And Tarkovsky’s filming of Solaris, a masterwork of SF film.
But, most times, I just don’t buy it. A biological intelligence would have evolved — by definition. And the constraints of evolution are universal. Cultures can grow into dizzying varieties, of course, and as such resist explanation; but, in the end, each must obey the constraints of biology, or the culture will perish, and this provides the common foundation that means understanding must in principle be possible. Just so, in the end, we can penetrate the purposes of an ant or a vampire squid, and we can penetrate the reasoning of a Yanomamo or Heroic-Age Greek.
I wonder if the idea of the incomprehensible alien is not a part or product of that greater cliche — the Great Cliche, we might call it: the lazy pessimism of contemporary SF literature. All is miserable in the future, our most awarded writers tell us. Even those inclined not to people the future with cannibals roving sunken cities are likely to portray the future as at best incomprehensible (the singularity!). This social and political pessimism bleeds over to an epistemic pessimism. And yet, the evidence is against this misery mongery.
So there is here an interesting challenge: SF that is optimistic, while realistic; that portrays aliens that are genuinely strange, but not incomprehensible.
This is a theme (or is it a meta-theme?) that I want to explore more.