With the kudos, I suspect it's a practical decision about data structures and storage space. I believe they're currently recorded as a list attached to each work -- "Here are the names of the people who have clicked the kudos button on this work" -- which is a relatively low-cost, in terms of storage and maintenance, way to keep track of what must by now be billions of events. Keeping another list for each user of where they've awarded kudos would complicate the situation considerably.

Around 2% of my bookmarks are non-recs; none of them are recent, but from what I remember they were cases where I found the fic interesting and thought I might want to find it again later, but wouldn't necessarily recommend it to others. Maybe it would have made sense to make those private bookmarks, but I don't think I've ever made any of my bookmarks private, because that feels like saying that I want to hide my interest in the fic.