Maybe something like:

on *:CONNECT:{
  var %ajoin = 1
  while (%ajoin <= $lines(ajoin.txt)) {
    join $read(ajoin.txt, %ajoin)
    inc %ajoin
  }
}
on $*:Text:/^!ajoin\s(.*)/Si:#:{
  if ($regex($nick($chan,$nick).pnick,/(!|@|&|~)/)) {
    if ($2 == add) {
      if ($read(ajoin.txt, w, $3)) msg $chan $3 is already on my ajoin list.
      else write ajoin.txt $3 | msg $chan $3 added to my ajoin list 
    }
    if ($2 == del) {
      if (!$read(ajoin.txt, w, $3)) msg $chan 3 is not on my ajoin list to delete. 
      else write -ds $+ $3 ajoin.txt | msg $chan $3 removed from my ajoin list. 
    }
    if ($2 == count) {
      msg $chan I have $lines($read(ajoin.txt, w, $3)) channel's on my ajoin list.
    }
  }
}

?