How do i create an array of ALL players and loop though them all

You've quoted both. Ahem, anyway...

I won't go as deep as providing you with the full code to copy&paste, so here's a couple of examples for you to understand what I (we all?) mean and, hopefully, use that knowledge right:

PHP:

$config = new Config($dataFolder . "players.json");

//So here's your rank duration and command cooldown time. Both of these values are in seconds.
//You may set these values in the code, in a config or even in your rank command...
$rankDuration = 86400; //24 hours
$commandCooldown = 43200; //12 hours

//As far as I understand, In your command you should check for the cooldown time and if it's been surpassed, the player can use the command again.
//The expiration time of player's rank can add up (if cooldown time is less than rank's duration).
public function execute(CommandSender $sender, string $commandLabel, array $args) {
    $currentTime = time(); //Here's a current timestamp. Saving it to not use time() too often.

    $playerConfig = $config->get($sender->getName(), [
        "expires" => $currentTime, //Fill the default expiration date with a current timestamp.
        "cooldown" => 0
    ]);

    if ($playerConfig["cooldown"] > $currentTime) { //Here's your check...
        $sender->sendMessage("HEY! Don't use this too often!");
        return;
    }

    //Now we should check if player's rank has expired, just in case it has. We don't want to add 24 hours to a timestamp of two days ago, if player has waited two days before getting his rank again.
    if ($playerConfig["expires"] < $currentTime) {
        $playerConfig["expires"] = $currentTime; //If it did expire, fill it with the default value - current timestamp.
    }

    $playerConfig["expires"] += $rankDuration;
    $playerConfig["cooldown"] = $currentTime + $commandCooldown;

    $config->set($sender->getName(), $playerConfig);
    $config->save();
}

//When a player joins you should just check if their rank has expired.
public function onPlayerJoin(PlayerJoinEvent $event) {
    if ($config->exists($event->getPlayer()->getName())) {
        if ($config->get($event->getPlayer()->getName())["expires"] < $time) {
            //Remove the rank.
            $config->remove($event->getPlayer()->getName());
            $config->save();
        } else {
            //If the rank's yet to expire, set your timer here or add the player to a list for your timer.
            //...just in case if it expires when the player is online.
        }
    }
}


 

Yes, I want to get good performance out of my server, but I don't understand how to use time()

 

PHP:

time(); //Somewhat like 1527855650
$timeThen = time();
sleep(3); //Wait 3 secs
$timeNow = time();
$timeNow > $timeThen; //true
$timeThen < $timeNow; //true
$timeNow - $timeThen; //3

 

That's somewhat helpful, but doesn't sleep() freeze the whole server?

 

It does, I wrote that as an example, it would work fine in a standalone script.