Why not physical note cards?
Lots of people, including Ryan Holiday still use physical note cards. They do this because the actual effort of having to hand write something makes them think. It avoids long and stupid intellectual masturbation (like this note!) and focuses on important content.
Why won't I use physical note cards? I used to do a lot of physical writing, filled up notebooks. I am aware of the thinking power of physical writing, but I've mostly replaced it, and I think, even improved it, by doing lots of keyboard writing. Plus my stuff is more searchable this way, and I always have a device with me to take notes, don't have to carry around a pen, can re-org/re-write at will. I will still miss the ability to doodle, mind-map, draw arrows, etc., but this wasn't something I did all the time even when I was spilling lots of ink, it was mostly to-do's and rants.
The ZK structure is what I've always missed.