Notes aren't just for reference. The act of taking notes (even if you never directly reference them again in the future) improves recall and understanding of the material for most people.
This was primarily the reason I started taking notes - I really had no plans to use them as references.
However, three factors have changed my outlook on this: 1) full-text indexed search, 2) cloud storage, and 3) low barrier to entry (I have found an organizational style that makes it easy for me to start writing at a moment's notice, without worrying about how to store/organize until later).
Full-text indexing is a huge deal, because I will often remember a certain combination of words or a particular term used in reference to some concept. Cloud storage ensures that I am almost never without my notes.
Add in the fact that if you make it easy enough for yourself to start writing, you will naturally end up with a lot of content about concepts you find difficult, and you'll skip the stuff you know well. The end result is a fully-searchable set of textbooks written specifically for your brain that you can always refer back to.
Sometimes, even if I'm not looking for a particular note, I'll crawl through a few old notes on any random subject in my notebooks and it will give me a new perspective on a problem I'm trying to solve, or remind me of something I wanted to try/research but didn't get around to.
