is there any good reasons for not having these docs, besides being a lot of work?

Recently, we've been considering switching to node based materials, and when that happens these docs would become obsolete. No idea when, or if, that's likely to happen though.

and when that happens these docs would become obsolete.

At least the current implementation of NodeMaterial uses the existing shader chunks e.g.

However, I think documenting NodeMaterial first (the different node types and how to use the system in general) might be more beneficial than documenting the low-level shader chunks.

I find that we can use string ‘void main() {‘ in most of shaders both for adding new uniforms and structs and for adding calculations inside main() function. Since .onBeforeCompile() looks like hack, we can describe this hack too.

Shader chunks have existed for a long time, and may not be going anywhere in the near future. It would be nice to document them. +1

However, this can also be done outside of the core/repo.

While a node based system might require documentation for something like MathNode one probably does not need to document the + - / : operators for GLSL, at least not in the context of three.js since they are universal for all GLSL. The chunks that @Mugen87 listed, are fairly unique and could benefit from some documentation, or at least inline comments.