Let's say I want to remove the User menu item from Wagtail settings menu.

All I need to do is to put this hook into wagtail_hooks.py file of my Wagtail CMS app:

from wagtail.core import hooks

@hooks.register("construct_settings_menu")
def hide_user_menu_item(request, menu_items):
    menu_items[:] = [item for item in menu_items if item.name != "user"]

Start the Django server, and you should see no User menu item under Settings.