One key strategy to avoid this kind of note graveyard forming is to interlink notes. That way seeing a note can essentially lead you to wiki-binging through old ideas, trains of thought or re-stumbling on reference you thought was interesting once upon a time.
The value of interlinked notes is showcased by the late German sociologist Niklas Luhmann's notetaking system which he used to rediscover things he'd forgotten. His knowledge base consisted of ~90,000 index cards that were apparently worth referring to because of the wiki binge type effect his hyperlinking system allowed.
https://www.lesswrong.com/posts/NfdHG6oHBJ8Qxc26s/the-zettel...
https://www.amazon.com/How-Take-Smart-Notes-Nonfiction-ebook...
It's a bit like touch typing - it takes substantial active effort at first.
Have you ever found yourself looping over a few pages too many times, or that a book is too difficult to digest? Or did you have to move a few chapters ahead to understand an early part of the book? This is where notes are extra useful. This is especially the case for math, science, technical books, or journals.
Some books are not suitable for note taking. Anything where the content can be summarized into powerpoint slides. Self-help or anything that's a best seller are often simplified enough for anyone to read. Story books are designed to be read without notes, and that often include historical and biographical.
I wonder if part of it might be because I write slowly and tend to focus on my penmanship (unknowingly).
Not criticizing note-taking; just offering another perspective.