Manual:$wgImplicitGroups

Details
$wgImplicitGroups is an array of groups that aren't shown in Special:Listusers and on a few other places. Note that they can't be assigned through Special:Userrights.

Syntax example
// defining a set of user groups which should not be shown $wgImplicitGroups = array('*', 'user', 'autoconfirmed', 'emailconfirmed', 'sysop', 'bureaucrat', 'bot'); // adding a single user group to an existing set $wgImplicitGroups[] = 'bot';

Note
It would hide only group names in the menu, not the users themselves.