CMW pre-filters the items on a defined Custom Menu before passing them through to WordPress. Since the WP Cart Menu item is not on the Custom Menu at the time that CMW runs, CMW can’t do anything about it.
Plugins like WP Menu Cart use filters within the WordPress processing (ie. within wp_nav_menu()) to add items to the menu, so whatever they do to the menu is done after CMW has completed its filtering.
You have a few options, one of which is to add a style that hides #wpmenucartli when it is within CMW output, maybe something like…
.widget_custom_menu_wizard #wpmenucartli { display:none; }
Another option is to add your own filter on 'wpmenucart_menu_item_wrapper' – one of WP Cart Menu’s – which selectively returns an empty string – the tricky bit here is how you work out when you need to prevent the WP Cart Menu item showing and when you need to allow it to show! (Maybe allow it once then prevent it after that? Depends where your CMW instances are on the page.)
