I see, this is interesting! It really depends on what kind of files are you talking about, I think.
For instance, you CAN download a .json or other text-file-like formats to your game, then write/overwrite a file that already exists, but if you're talking about graphics/sounds/code, since it's all in the package.nw file, you'd have to re-download your entire game basically.
The best way to achieve an updatable game with Node-Webkit would be having a separate application that would be able to open the package.nw file, change it's contents, then re-zip it, I think.