$msc=microtime(true);

$chat_alg = mysqli_query($con, "
    SELECT sid, COUNT(*) as frequency
    FROM plays
    WHERE time > NOW() - INTERVAL 3 DAY && sid != ''
    GROUP BY sid
    ORDER BY COUNT(*) DESC
") or die(mysqli_error($con));

while($row_chat_alg = mysqli_fetch_array($chat_alg)) {
    $chart_songs[] = $row_chat_alg['sid'];
}

$imploded_songs = implode($chart_songs, ',');

$projects = $dbh->query("
       SELECT * FROM music
       WHERE perms != 'c' && sid IN($imploded_songs)
       ORDER BY FIELD(sid,$imploded_songs)
       limit 50
");

$msc=microtime(true)-$msc;
echo ($msc*1000).' milliseconds';

...
Time taken: 9.5310001373291 milliseconds

SELECT m.*
     , COUNT(p.sid) frequency
  FROM music m
  JOIN plays p
    ON p.sid = m.sid
 WHERE p.time > NOW() - INTERVAL 3 DAY
   AND p.sid != ''
   AND m.perms != 'c'
 GROUP
    BY m.sid
 ORDER
    BY frequency DESC
 LIMIT 50

SELECT *
   FROM music
   INNER JOIN (SELECT sid, COUNT(*) as frequency
               FROM plays
               WHERE time > NOW() - INTERVAL 3 DAY && sid != ''
               GROUP BY sid
               ORDER BY COUNT(*) DESC) as innerresult ON music.sid = innerresult.sid
   WHERE perms != 'c'
   ORDER BY music.sid
   limit 50