No, I don't think so. "Hiding", in every desktop system I know, would in effect be minimizing or hiding it to the system tray, both of which is to my knowledge impossible in JavaScript, even using the window.resizeTo function.
If you're building a web application for a limited range of users, and you can control what software they use, it could be possible with Mozilla Prism, a lightweight browser that displays web applications without the usual browser interface. But that's something entirely different and probably not what you're looking for.