Visualizations are just one aspect of documentation, so I would recommend looking into how you organize your documentation, and build visualizations to support that. This is, after all, what I think you are really going for: just better written explanatory documentation, with useful organization.

The divio system is a good place to start, IMO, when it comes to organization: https://documentation.divio.com/

So, I would treat a visualization used in an explanation-style document very differently from a reference guide. One is intended to illustrate a concept quickly, another is intended to be precise. I don't think you'll see a single "visual system" ever take over, largely because documentation can have very, very different goals for the reader.

Visualizations in reference guides are (unfortunately) rare. I happen to like the approach taken by project reactor, embedding visuals into java reference docs: https://projectreactor.io/docs/core/release/api/