I want to use node.js to eventually keep track of highscore data, and I need it to use:

fs.readdir()

Does itch.io allow me to make use of node?

We don't run any server-side code for our users. The code you provide to be embedded for HTML must be for the browser. That's not stopping you from hosting your own infrastructure and communicating to it with your HTML game though.

In the future we hope to have a high-score API though, which should handle your particular use case.