I've changed the hload to...

Code:
hload -n twitchEmotes emotes.txt


... to stop the table from seeing the emotes as numbers. Now when I view it I see them as...
Code:
*Kappa*


If my understanding is correct, you suggested I format the emotes that way so the script checks before the emote and after for more instances of emotes?

Code:
ON @*:TEXT:*:#: {
  if ($nick isop # && $hfind(twitchEmotes, $1-, 0, w)) {
    INC %ecount
    if (%ecount >= 5) {
      msg # Stop spamming emotes, $nick $+ !
      ;msg # .timeout $nick 120
    }
  }
}

This was to test if it could read that way. Kappa would not trigger the warning, but *Kappa* did. A message of "*Kappa*" would increase the count, but "*Kappa* *Kappa* *Kappa* *Kappa*" would not increase the count.

Off to try more.