>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?").

Isn't that exactly what the point of a memex-like system is? Instead of simple X-Y links, you get 3-tuples such as (X, "can cause", Y).