Another point is that every platform-specific plugin makes it harder to port your project. Ideally a project designed for node-webkit would just export to the web or another platform like Windows 8 without losing too much functionality, or throwing errors on startup due to missing files on disk or whatever you relied on. So I'd want to very carefully design any node-webkit specific features and try very hard to integrate them with what can already be done in a browser.
For example, take file I/O. Chrome supports an experimental filesystem API and most modern desktop browsers support IndexedDB, both of which are suitable for storing large amounts of data in a filesystem-like arrangement. If we just quickly bolt on some file I/O functions to node-webkit via a platform-specific plugin, it's likely any games you design using it will be broken when ported to other platforms. However, if we very carefully design a file storage plugin that uses different storage backends (filesystem on Chrome, IndexedDB on Firefox/IE10, disk on node-webkit) then your game should still work in web browsers even though it uses local files. That's far more valuable than a single platform-specific hack - but it's also a lot more time consuming to design. The same goes for most other features you'd want from node-webkit.