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
$wgImplicitGroups = array('*', 'user', 'autoconfirmed', 'emailconfirmed', 'sysop', 'bureaucrat', 'bot'); $wgImplicitGroups['bot'] = false;

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