It's not just about the speed of executing Javascript code. The UI is rendered with the browser's rendering engine. I've used Atom and it was a disaster, so I no longer trust any desktop applications written using that technology.
I think that if you're going to write a desktop application, you should either use your native platform's APIs or pick a GUI toolkit that can give you a native look and feel. It'll give you a fast UI that looks and behaves consistently with the rest of the user's environment.
Please don't write off an entire technology because of one slow early release of an example of it. There should be better ways of utilising native UIs, I'll give you that.
It may be fast, but I don't see a scripting language winning out compiled native code on speed. Don't get me wrong, I don't think the speed difference is large enough that it matters in something as simple as a basic UI.
I think that if you're going to write a desktop application, you should either use your native platform's APIs or pick a GUI toolkit that can give you a native look and feel. It'll give you a fast UI that looks and behaves consistently with the rest of the user's environment.