What should be the anatomy of your rig? Hierarchy is important because it serves two purposes. Certain decisions are made for the sake of organisation, other decisions have effects on function and performance. Some decisions can serve both purposes and could be argued to have a correct answer, but other times you can only serve one of these purposes at a time. And a decision will need to be made whether a little performance is worth sacrificing for better organisation, or vice versa.
Organisation doesn't necessarily just mean easier to look at and sort through. It could also be a matter of putting components of your rig in a place in the hierarchy which will accommodate scripts you know will be run on the rig in future.
If you know that your animators have a script they run to expose or hide all the joints, and you know that script works by finding the joints group and hiding/unhiding it then obviously there needs to be such a group and all the joints need to be within it.
If you wanted to reform that aspect of the hierarchy within a pipeline, they would need to change their script to identify the joints some other way.
So how you arrange your rig hierarchy is often about the needs of people further down the pipeline.
You might have heard people arguing online about the merits of broken or unbroken hierarchies. But this is misleading. All hierarchies are broken. It's a question of how much.
A rare example of a completely unbroken hierarchy is perhaps the driven skeleton that gets exported into videogame engines. But I don't know if that even counts as a "Rig" if there's nothing driving the skeleton.