I'd have to check again, but I looked for specific versions of a JS file and found it repeated multiple times throughout the forest of node_modules.
If side-by-side is desired, then just suffix the folder with a version name. foo.js-1.1 and foo.js-1.0 can be in the root and reused by every package that needs either.
Maybe it does that and I didn't understand what I was looking at.
It's quite naive about it, so it will copy them over and over again. Supposedly there are tools that make everything in node_modules symlinks to the same files.
It's not exactly an advanced and polished system, but it still has a feature that is hard to get with others.
