I realize now that perhaps I should have split my a topic in two: one for ux and another in bug as my main issue (disappearing bookmarks) is getting shadowed by the usability one.
I have in the meantime been poking at the bookmarks feature and found another bug, but I’m still lost at why bookmarks are randomly disappearing from /bookmarks. It seems to be more common with some topics than others for some reason, but I haven’t found a common pattern. To me what’s really strange is that after bookmarking something, it seems to display fine under /bookmarks for some arbitrary number of hours/days, until it disappears from there and is only “fixed” by removing the bookmark and bookmarking it again.
To be clear, this is not an issue with setting a bookmark reminder to delete the bookmark: no reminders involved, and the bookmarks are not getting deleted (they still show under /my/activity/bookmarks) — they are only missing from /bookmarks after a while.