Why: custom Taxonomy doesn’t appear in the custom menu? Because: set he screen options for your client

So you want to add your custom taxonomy to a menu. You probably have to alter your screen options to let the taxonomy appear in your ‘menus’ menu. However, these settings are user -specific. So if your client also should be able to change this menu, switch to your client’s profile and change the screen options accordingly. Or tell your client how it works…