I have a deep distrust of hierarchies, because they keep you trapped into a single model that keeps extending its authority, usuall without anyone explicitly deciding that it should do so. For example, the file system: once it was deemed hierarchy is the main metaphor for navigation, the structure persisted and was reused for organisation, ownership, access control and governance. And it became infrastructure we cannot easily remove before we could even question if it was right or not. And once it dominated, non-hierarchical things were retrofitted as glue, e.g.: symlinks, aliases, shortcuts... also, when's the last time you've used a tag?

The webs are so much more malleable, but they're also not free. All the 'good enough's you were that a hierarchy that was taking care of implicitly are now your responsibility to model precisely and make sure they're performant as well. Look at ReBAC, for example. It gives you expressive power, but it also forces you to reason precisely about relationships, graph traversal, consistency, and cost. Strikingly similar is GraphQL.

Interestingly, source code is hierarchical, but compiles almost immediately to a graph IR and most analysis and optimisations happen there. But almost nobody looks at a CFG/SSA graph directly. You author in a hierarchical manner, yet the operational substrate is a malleable graph.