For Academic writing like the creator of zettelkasten was, web method is much preferred.

For linear notes, the remedy is not really feasible, you'd have to go through everything thoroughly fixing unlinked notes.

For the 2nd, the 'failure mode' of the web note taker as you describe, that isn't really a problem. Notes are just tools/building blocks to writing or coming up with cohesive ideas/arguments. If you don't know what Y was for, its either irrelevant or you've found a gap in your knowledge you need to plug.