has anyone had particularly pleasant experiences graphically manipulating wide and/or deep structured data

Yes — working with complex scenes and meshes in 3d modelling tools, with tens or hundreds of thousands of faces, edges, and vertices. Though I'm not sure that's what you had in mind.

Literally anything works! How do they aggregate information/summarize it / let you access deeply nested data?

In a typical professional 3d modelling program, there are hundreds of different tools for working with your geometry (and other types of data too). Many of the tools work with a typical orthographic or perspective viewport, allowing you to move or transform the pieces of geometry directly. Some of these tools will change the way the mesh or its parts are displayed in the viewport, to help visualize the effect that the transformation is about to have. For instance, both sculpting tools and rigging tools have an area of influence with some sort of falloff, so they might color the vertices that are at the center of the effect (eg: bright red), then fade back to a more neutral color (eg: light blue) toward the outer edge of the effect. Other tools will introduce an entirely different representation to help you accomplish their task. For instance, when working with normal maps, there might be extra normal vectors added to the vertices or faces to show which direction is tangent to the surface. This is a difficult subject to talk about if you aren't familiar with the domain terminology, because these tools are so vast. It might be worth just watching someone making a 3d model, just to see how they work, even if you aren't entirely sure what they're doing at each step. This person is a good speed-modeller, and I enjoy watching them work, so you might too: https://www.youtube.com/user/Askguden/videos. In each of their streams, they start from nothing and quickly (relatively speaking — still takes a few hours, so you might want to skip around) build a highly detailed model.

thank you for the extremely detailed response! i will definitely check them out

SQL, datalog both provide ways to Manage lots of data. Specter in clojure, and lenses in haskell are both programming solutions I'm aware of for these types of issues as well.

haha that’s ok