@worrydream “bookshelf” is completely the wrong mental model. A “list of links” is like a list of postal addresses of places (hence web “address”) as a physical analogy, or the contents of their authors brains as a human analogy. Complaining about their contents changing/disappearing is as complaining that space/time/humans are “a disaster” (which admittedly may broadly be true).
“your bookshelf” is whatever personal archives you make of your favourite things (analogies: photos, notes, physical books), and therefore the solution is better personal archival tools. I’ve made a start — my website automatically takes an archive of every page I link to and stores it as HTML+HTTP headers in the filesystem, which has proven to be a quite robust format.
Of course if you actually have a practical idea about how to improve on the infrastructure of the web, speak up and/or build it :)