The custom fields menu item can be hidden. This can be done in several ways and it is done in the code of the site.
There is the ACF filter, explained here: http://www.advancedcustomfields.com/resources/how-to-hide-acf-menu-from-clients/
There are also other ways that the menu can be disabled or hidden. This is generally done so that clients do not have access to mess about with things they probably shouldn’t be messing with.
