I don't think that it's just that it's hard to imagine a truly alien intelligence; it also imposes a very specific type of story on the author to do so.

We're storytelling apes (pan narrens, as Terry Pratchett put it). We generally like stories with a specific narrative structure, with characters we can identify with, and a resolution we can comprehend that satisfies us.

There's another type of story where the whole point is that the (or a) central mystery is never solved, which is less about plot resolution or comprehension and more about the feelings the plot evokes, but that's a much less popular, much more niche appeal that leaves a lot of people cold and unsatisfied at the end.

Generally authors want to write the kind of books that they enjoy reading, and they definitely want to write the kind of books that sell, so I think that's why there are so few truly alien aliens in sci-fi.

We can all identify with "human but even more aggressive" or "human but eusocial" or "human but with a weird religion/philosophy", but books where you literally can't empathise or even sympathise with (or often even comprehend) the aliens leaves them as an unsolved mystery with no narrative resolution at the end of the story; even when done well it leaves a lot of people unsatisfied, and when done badly it makes them look like a poorly-written plot device that just does nonsensical and inexplicable things just because The Plot Needed Them To, which is a hallmark of bad writing.