The also-boughts didn't just disappear from book pages, though. They disappeared from other kinds of product pages. It's particularly frustrating when you're shopping for tools or something where you need to also shop for accessories. That sort of thing--accessories--is where the "frequently bought together" thing just isn't good enough because it doesn't give you enough options.
For me, the also-boughts didn't go missing until a few months ago. Then they were gone for most of this calendar year. Now, though, they seem to be returning. For example, Joe, I see seven pages of also-boughts on your Brothers in Exile page.
I've always held onto the belief--and this is just my own guesswork here, so take it for what it's worth--that the disappearing also-boughts was a symptom of server strain. The elements on the product page load individually, not all at once, and that tells me they're powered by different servers. When Amazon got into video streaming in a big way, I think they underestimated the server capacity they would need in order to keep the whole store running smoothly, and the result was the also-bought equivalent of rolling brownouts. And also-vieweds, too, because those would sometimes fail to load, too, and whatever else would occasionally go missing.
Other have postulated A/B testing, and I'm not going to discount that possibility, either. Until Amazon spills the beans about it, we're all just theorizing.
So no, I don't think the disappearing also-boughts have anything to do with KU due to the fact that they disappeared from other kinds of products, too, not just books, and they seem to disappear and reappear in a random fashion rather than as part of a discernible plan.
As for how the algorithm treats KU and rank, I have no idea. I'll leave that to the podcasters to suss out.