I've taken 3000 pages of notes in a linear, bullet-point fashion, and I also keep up with education research.
As far as I can tell, both in studies and in personal experience, the fiddly details of your note-taking schemes don't matter. The only thing that matters is attempting to integrate the information into a cohesive whole, which takes intentional thought.
With linear notes, there's a failure mode where links that should be made aren't; you can even walk around believing outright contradictions without noticing. But with a web, there's an equally bad failure mode where your knowledge gets diffuse and unstructured (instead of "X causes Y if Z", you get "X, Y, and Z are related. But... was Z the thing that caused X? Wait, but then what was Y for?").
Both of these reflect a failure to aggregate and chunk the information into hard tools, but no productivity system can magically fix that; it always takes time.