Code:
function numOfPlayersExceptVanished() {
    var num = 0;
    for (var i = 0; i < args.length; i++) {
        num += BukkitServer.getWorld(args[i]).getPlayers().length;
        num -= BukkitServer.getWorld(args[i]).getVanished().length;
        if (i + 1 == args.length) return num.toFixed(0);
    }
}

numOfPlayersExceptVanished();
Save this as "number_of_players_except_vanished.js" on /plugins/PlaceholderAPI/javascripts/


Code:
number_of_players_except_vanished:
  file: number_of_players_except_vanished.js
Add this to javascript_placeholders.yml