To, že je premenná globálna, musíš deklarovať vnútri funkcie.

$subsections;
$subsections_count;
	
function add_subsections($id, $conn1)
{
  global $subsections;
  global $subsections_count;

  $subsections_count++;
  $subsections[$subsections_count] = $id;
    
  $sql = mysql_query("select * from shop_sekcie where main=$id order by sort", $conn1);
  while ($line = mysql_fetch_array($sql)):
    $id0 = $line[id];
    add_subsections($id0, $conn1);
  endwhile;
}