If any of your users have already customized their own categories and tags, hiding that pencil isn’t going to reset what they have already selected for their own menus. As others have pointed out, user customization of those sections is intended to be encouraged.
Just in case you may not be aware, users also have the ability to create their own personal menu sections with their own links by clicking the + at the bottom of the navigation sidebar menu. However, if you as an admin create a custom menu section that is visible to everyone, non-admins cannot change any of it.