I love this idea and could really use it. A few ideas on how I personally would like it to work:

1. The nested nodes should act a little like a unity prefab. You should be able to reuse it and if you make changes to it, there should be a way to apply those changes back to the "prefab." I wouldn't necessarily want it to auto-update other shaders, but it should be easy to import/apply the updated prefab in other shaders that use it, rather than deleting and re-adding. This implies some form of library either in the project or saved globally to share between projects.
2. I agree with Kajfa. The nested nodes could be visually grouped into a container that would be zoomed out by default with regular sized inputs/outputs on the container. that way you can kinda see what's going on, but you can also zoom in to edit.
3. I think this is obvious, but I would like to be able to name them and have them show up in the list of nodes on the right, as well as in the shortcut menus (when you press a single letter), maybe at the bottom.

Unrelated, but huge congrats on the award at Unite!