There is an option in the backend to hide empty category this option is only available in the paid version, for free version all the category will be shown even if they are empty
If you want to change the layout of the Menu page then you can do that by activating an option in the backend. If you activate this option then you can overwrite the template page in your theme like you do for WooCommerce. but if this option is not active then the template page overwrite won’t work.