npm v3 already uses the 'flat by default' design, so the node_modules folders aren't that different.
I made a quick comparison here: https://gist.github.com/alexanderGugel/a10ed5655d366875a280
Basically ied uses symlinks in order to resolve circular dependencies, while ied exploits the fact that require "falls back" in the directory structure.
> Basically ied uses symlinks in order to resolve circular dependencies, while npm exploits the fact that require "falls back" in the directory structure.