I use the desktop version of Draw.io + some custom code to make the diagrams searchable: https://github.com/JesseAldridge/draw.io-convert

I do think a truly useful knowledge repository will fundamentally need to be a graph structure. This roughly reflects the neural connections in the human mind -- knowledge itself is a graph structure.

Draw.io is the best diagramming tool I've found, but it still kind of sucks in a lot of ways. I've started working on an alternative: https://github.com/JesseAldridge/consideration

The key features I'd like to add are multi-user collaboration and search across many diagrams.