I really don't understand why people keep saying this, it's simply not true. Node works fantastically on Windows. I've yet to come across a library that won't work on my Windows box (barring obviously platform specific stuff). Node-gyp works fine too, and many libraries with native code offer Windows versions.
Especially when comparing to e.g. Ruby or Python, it's a world of difference. With Ruby you can't even use bundler on Windows and then deploy on Linux.
It seems all the basic fundamental design choices of Node and NPM were made with portability in mind. I'm frankly quite impressed.
Source: been running teams doing frontend and node for almost 3 years now, every team had at least one Win dev and at least one OSX dev, every team deployed to Linux. 0 problems, ever.