Yea. .Bat/.VBS are Windows exclusive scripting technologies. However, Linux and MacOSX feature similar batch scripting engines.
At least on MacOSX, it will be pretty easy to create an update script that will keep your old files. Node-Webkit for MacOSX simply copies and replaces existing files inside the .App container, while Node-Webkit for Linux and Windows concatenates two or more binary files.
As for multiplatform installer builders, you might want to take a look here.
Isn't the cross-domain issue still persistent with your Ajax implementation? Wouldn't be worth much if it didn't allow for cross-domain actions.