No kidding. When I was heavily contributing to Julia's Pkg (which uses roughly the same model for modules as NPM, at least in terms of the file system), our test suite would run roughly an order of magnitude slower on Windows. This was very annoying on days where a lot of PRs where in the pipeline. I poked around the problem about for a while, and eventually came to the same conclusion (but I'm no Windows expert).

Eventually, I worked around the problem by using a caching system to avoid blowing up the filesystem. It was necessary at the time, but it never felt like a satisfying solution. I wonder if anyone has the knowledge to make native Windows go fast on e.g. a large number of sequential git clone operations.