Paper systems don't have to be "100% paper". All you need is the metadata from your notes. You can give each note a number and then add that number plus a couple tags and a short description to a spreadsheet. Alternatively, you can take a picture of the note and add that to your digital system. It's not how I currently do things, but it's infinitely better than a primitive digital system where you take notes and never touch them again.
Bullet Journals are perfect for that ( https://bulletjournal.com/pages/book ), I'm still using them for managing my personal life (ideas, goals, progress on stuff, daily journals, etc). Having knowledge base in digital format is better in many ways, but IMO nothing beats notebooks when it comes to solving problems and thinking.
Paper systems also suffer from "never touch them again", and adding a digital index only provides superficial search ability.
I'm not saying paper systems don't have a place - people have put them to use for centuries after all. They do have very real limitations though, and to be really useful require more ongoing work than many people are willing to put in, especially if they grow to an appreciable size.
