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.