maybe use hash for this instead of filling up ur var list

here is a fast rewrite using hash trying to keep it at what you have. added a delete command an you may want to add a flood control an some checks, but w/e

on @*:text:!joinmsg *:#: {
  if ($nick isop #) {
    if ($2 = on || $2 = off) {
      .hadd -m joinmsg $+(conf,.,$network,.,#) $iif($2 = on,on,off)
      msg # Joinmsg $+(,$hget(joinmsg,$+(conf,.,$network,.,#)),.)
    }
    if ($2 = set || $2 = del) {
      $iif($2 = set,.hadd -m joinmsg $+(text,.,$network,.,#) $3-,$iif($2 = del,hdel joinmsg $+(text,.,$network,.,#)))
      msg # Joinmsg $iif($hget(joinmsg,$+(text,.,$network,.,#)),set.,deleted.)
    }
  }
  else { msg # $nick - Only channel operators may use this command. }
}
on !*:JOIN:#: { 
  if ($hget(joinmsg,$+(conf,.,$network,.,#)) && $hget(joinmsg,$+(text,.,$network,.,#))) {
    msg # $hget(joinmsg,$+(text,.,$network,.,#)) 
  }
}
on *:start:{ $joinmsgstartup } 
on *:connect:{ $joinmsgstartup }
on *:exit:{  $joinmsgclose } 
on *:disconnect:{ $joinmsgclose }
alias -l joinmsgclose { .hsave joinmsg $qt($scriptdirjoinmsg.hsh)  } 
alias -l joinmsgstartup {  
  if (!$hget(joinmsg)) { .hmake joinmsg 100 } 
  elseif ($exists($qt($scriptdirjoinmsg.hsh))) { .hload joinmsg $qt($scriptdirjoinmsg.hsh) } 
}