> Are people really making projects with dozens (hundreds? more?) of dependent libraries?
Yes.
> Are there aspects of the language or runtime that reward multiple layers of configuration management?
A significant fraction of the node community likes to split their project into really, really small packages and treat them as if they're independent even if they come from the same source repo and tend to get used together. As an example, the popular collection processing library Lodash publishes a package for each method and people actually do depend on individual methods.
There are two major rationales for this. The first is that JS is a dynamic language and in dynamic languages, smaller chunks of code are easier to reason about than larger ones. The second is that the JS community as a whole cares more about artifact size than pretty much any other community. Having smaller packages allows you to produce a smaller payload without having to rely on techniques like tree shaking.
I find micro packages maddening but people give me their code for free and it mostly works so I don't complain about it that much.