If they need to interact with the host OS, someone needs to write those native plugins, and that won't be in JavaScript, as the Github repository for Electron clearly proves.

In the end is all about using an hammer for everything.

You can write Qt apps entirely in C++ or entirely in QML (of course you can mix and match both... in my experience whatever the environment you always need to resort to native modules at some point anyways, eg numpy, opencv, etc and Qt makes exposing them to Javascript dead easy).