Apart from the dll that tidy recommended (which I haven't tried), there are two fast alternatives: either use $comcall() (and a few aliases) instead of $com(), so that the process check is done in a separate thread, or move some of the work outside of mirc (in a .vbs for example). Unfortunately, both ways would mean rewriting your script almost from scratch.

An effective way to speed up your script (although not as much as the previous two solutions) without changing it too much is to modify $isprocess to check for two or more processes with a single ConnectServer/ExecQuery call. I modified $isprocess and /coolmonnetwstats accordingly, you can give them a try:
Code:
alias coolmonnetwstats {
  var %cpu $left($dll(darkenginex.dll,cpuload,_),3)
  ; if wscript.exe isn't running but coolmon.exe is, $isprocess returns 2
  ; (10 in binary: the first bit, which corresponds to the first process 
  ; that you specified (wscript.exe), is 0. The 2nd bit (coolmon.exe) is 1)
  if (%cpu <= 60 && $isprocess(wscript.exe|coolmon.exe) == 2) {
    write -cn "C:\Program Files\CoolMon\extensions\CoolMon Network Result Time.txt" $asctime(HH:nn:ss)    
    run "networkStatus v2.1.vbs"
    inc %counter.netwupdate
    inc %counter.netwupdateloop
    if ( %counter.netwupdateloop = 500 ) {
      echo -ts CoolMon Network Status-update n° $+ %counter.netwupdate completed...
      %counter.netwupdateloop = 0
    }
  }
  .timernetwstats 1 5 coolmonnetwstats
}
alias isprocess {
  ; checks if process(es) exist(s)
  ; $isprocess(<process1[|process2|process3|...]>[,N]) - returns 1 if there's an Nth process for <process>, otherwise 0.
  ; if more than one process names are specified, N is assumed 1 and $isprocess() returns a number where each bit
  ; represent each process in the list: if the Mth process in the list isn't running, the Mth bit of that number will 
  ; be 0, otherwise 1. To check if process3 is running, for example, you'd do either this:
  ; if ($isbit($isprocess(proc1|proc2|proc3),3)) 
  ; or this:
  ; if ($isprocess(proc1|proc2|proc3) & 4)
  ; (if you don't understand the 2nd example, just use $isbit())
  ; example: if ($isprocess(mirc.exe,1)) { .echo -q $endprocess(mirc.exe,1) }
  if ($isid) {
    if ($2 !isnum 1- || *|* iswm $1) { tokenize 32 $$1 1 }
    var %a = a $+ $ticks, %b = b $+ $ticks, %c = c $+ $ticks
    .comopen %a WbemScripting.SWbemLocator
    if ($com(%a)) {
      .comclose %a $com(%a,ConnectServer,3,dispatch* %b)
      if ($com(%b)) {
        .comclose %b $com(%b,ExecQuery,3,string,SELECT Name FROM Win32_Process WHERE Name =" $+ $replace($1",|," OR Name ="),dispatch* %c)
        if ($com(%c)) {
          var %result = 0
          if *|* iswm $1 {
            var %i = 1, %f = $calc(2^ $numtok($1,124) -1)
            while %result != %f && $comval(%c,%i,Name) != $null {
              %result = $biton(%result,$findtok($1,$v1,124))
              inc %i
            }
          }
          elseif if $comval(%c,0) >= $2 {
            %result = 1
          }
          .comclose %c
          return %result
        }
      }
    }
  }
}

/.timerQ 1 0 echo /.timerQ 1 0 $timer(Q).com