That's great, but it's not without cost. Here, the cost is you end up with deeply-nested directory nodes (which breaks Jenkins ability to properly purge the directory after a job). Node modules are also extremely liberal in the number of files they create -- even a "simple" app using just a few common modules could end up with 1k+ extra files. This can produce problems in your IDE, as well as with your source control or continuous delivery systems, among other things.

So, it solves some headaches, and creates others.