Organizing vertex groups used to be a nightmare because you couldn't give them a folder structure in native Blender.

This is where Vertex Group Collections saves the day and allows for full control over your vertex groups. Bring structure to the chaos, a folder structure, that is.

With this new management system you can rename and organize which vertex groups go in which folder, including the benefit of subfolders for full tidiness and ease of use. It's been stress tested up to 1000 vertex groups on a model, where performance can degrade significantly. But it's doubtful one would reach even half of that number.

Shape Key Collections, another addon, also allows for a folder structure - https://blendermarket.com/products/shape-key-collections