I've had precisely your reaction, and am stoked to share my enthusiasm for Roam (https://roamresearch.com) -- a graph-based system for codex / memex / personal knowledge-base / zettelkasten++
As a backend engineer, I just think: "Man, this data is just sitting in a db somewhere for any engineer to grep." Until we get to a point where everything is just encrypted by default, I just can't see myself trusting software like this.
But, yeah, when it works it's very nice indeed.