You generally use either mqtt or the zwavejs integration with zwavejs2mqtt. If you use both you will indeed get duplicates if all devicez.
Unless you need mqtt outside home assistant, I’d recommend disabling mqtt in the zwavejs2mqtt control panel, and just use the zwavejs integration in Home Assistant. The integration uses websockets, discovery works better, and it’s quicker.
I posted recently about this here.
Also see this post for additional context and information