Putting this in the functions or bp-custom.php files did not work.
I finally managed to get the admin and any other user excluded from the members directory by modifying the bp_had_members query that was already in my members-loop.php file.
<?php if ( bp_has_members( bp_ajax_querystring( ‘members’ ).’&exclude=1,3,25′ . ‘&type=alphabetical&per_page=30’ ) ) : ?> <!– &exclude= user_ids of the people you want to exclude –>
By adding just this, it also removed the users from the total members count.
Note: I do not use friends or activity feeds on my site, so I have no idea if it hides from them, but I suppose it wouldn’t.
I have been looking high and low for the answer to this with my limited PHP knowledge… and wanted to share it back so other people could learn from it too.