mIRC will always return 1 for $script(0), because it's impossible to have "0" scripts loaded (a blank file will be automatically loaded). It's more likely that nothing (of importance) is in this file.
More importantly, scripts can't control contents of a nicklist, only the colors, so it would be extremely unlikely that the user has a script doing this.
I would go about this another way, because it seems like there could be a communication issue here:
exeCutive, can you describe more specifically what you are seeing? It would be helpful if you could answer as many of the following questions as possible:
1. You say the "number of users increases"-- where are you observing this increase?
2. When exactly is this increase in users happening?
3. Did any nicks join after the QUIT?
4. When do the nicks show up in the nicklist?
5. Are they coming back after another user joins, or are they not being removed at all?
6. Is this happening on a single channel, or all?
7. If all, can you join a small channel (1-10 people) and reproduce this?