Atom's performance problems are not because of Node, they're because they render with HTML, loading your whole text documents into the DOM as hundreds of thousands of separate elements.
Using Node JS as the backend to a proper native rendering system would work fine, and in fact if the application was written to properly handle everything asynchronously, it may well be faster than an app written entirely in the native language of the system.
No. I said it "may well be", because a naive implementation using a native language may block while doing IO and be less responsive, unable to do other things while waiting for external stuff to happen.
Perhaps I should have said "may well be more responsive than".
So, you don't actually know anything about whether native apps block on IO? (I doubt they do on any modern version of Windows, OS X, Linux, Android, iOS or Windows Phone.)
Using Node JS as the backend to a proper native rendering system would work fine, and in fact if the application was written to properly handle everything asynchronously, it may well be faster than an app written entirely in the native language of the system.