I know this may be badly scripted but i only done it quickly, there is a single error which i have found. Once you unhide a channel using /window -w #chan it still says its hidden untill the next time you use check. Just click in a channel to hide it and type /check to see the channels you've hidden. Sorry for the messy scripting :P

Alias Window {
  if (h isin $1) {
    window -h $2
    set %hidden $addtok(%hidden,$2,44)
  }
  var %x = 1
  while ($gettok(%hidden,%x,44)) {
    echo -a -------- $+ %x $+ --------
    echo -a Hidden Chan: $v1
    inc %x
  }
  if (w isin $1) && ($2 isin %hidden) {
    window -w $2
    set %hidden $deltok(%hidden,$findtok(%hidden,$2,44),44)
  }
  while ($gettok(%hidden,%x,44)) {
    echo -a -------- $+ %x $+ --------
    echo -a Hidden Chan: $v1
    inc %x
  }
  Else {
    window $1-
    Halt
  }
}
Alias Check {
  var %x = 1
  while ($gettok(%hidden,%x,44)) {
    echo -a -------- $+ %x $+ --------
    echo -a Hidden Chan: $v1
    inc %x
  }
}
Menu Channel {
  Hide $active:$iif($active isin %hidden,Halt,window -h $active)
}