This isnt perfect it can be fooled by a script closing a pm. But for the average user it works pretty well.

Code:
alias -l query.window.list { if (!$hget(query.window.list)) { hmake query.window.list } | return query.window.list }
;
on *:CLOSE:?:{ hdel $query.window.list $+($cid,$cr,$target) }
;on *:CLOSE:*:{ !.echo -q $input($target .ALL. closing,o) | if ($target == Status Window) { while ($hfind($query.window.list,$+($cid,$cr,*),1,w)) { hdel -s $query.window.list $v1 } } }
;
on *:OPEN:?:*:{ opened.query.window $target }
on *:ACTIVE:?:{ if (!$hget($query.window.list,$+($cid,$cr,$active))) { opened.query.window $active } }
;
alias opened.query.window {
  hadd -m $query.window.list $+($cid,$cr,$1) 1
  echo -s Just opened $1 query window
  ; any other code you like to do on a queryu window opening here.
}



another option is to do this (along with your ON OPEN)

Code:
alias query {
  if (($0) && (!$window($1)) {
    query $1-
    if ($window($1)) { echo -s Just opened $1 query window }
  }
  else {
    query $1-
  }
}


but if someone uses /!query it well bypass it.