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I do scan my notes periodically - but if I'm honest I very rarely find that I need to go over them again.
Resist trying to find the perfect system. Forgive yourself, and do what comes naturally.
I mostly use digital notes. Except when I use paper. I then use the Scanbot iPhone app to store paper notes digitally in my notes app of choice (Apple Notes for personal, Bear Notes for work, in my case).
I have repeatedly tried to convert over to pure digital note taking, but have not been able to. This is in the context of active learning (classroom, live video lecture, etc. where I cannot pause). As you said, there is nothing like the convenience of sketching out a graph, quick comments on the margins, drawing arrows to point at stuff, etc. I know there are digital solutions to everything I mentioned, but none of t…
Active learning is definitely a weak area for digital note taking. When I use a computer in this context, I tend to 'take notes' with extreme shorthand and polish it up later - however at that point I've struggled/failed to remember to include some key insight or diagram.
As @ziddoap mentioned, the main drawback to digital note-taking and learning is that it is not as natural to engage with your notes (drawing, making comments, etc).
But there are other aspects of digital notes that make them superior to hand-written ones when it comes to learning. It's just that, imo, it hasn't been optimized for yet.
Specifically, take spaced-repetition. One of the most proven ways to improve memory. It'd be easy to integrate such a system inside a note-taking app - and that would help ensure note-takers self-test themselves and periodically review their notes. But no note-taking app is doing that, at least not built-in.
So that's why I've started working on this myself. The app is called Studbits (http://studbits.com), and the idea is simple: we let you create flashcards alongside your notes and then remind you to review them with a spaced-repetition system.