I think the beeps should be optional as well, or only beep the first few characters after the threshold.
Making mIRC beep only a few times after the threshold sounds like a good idea. I will see if I can implement that for the next version.
If nothing else, just disable the beep if you have mIRC's split long message option enabled.
I think this is already the case - if split long messages is enabled, mIRC should not beep when you pass the threshold.