Personally, I think the beeps should be optional as well, or only beep the first few characters after the threshold. If you are still typing after that point, then it should be clear that you mean to do so and the beeps can stop. I think just having them optional is the best thing anyhow. I'm a little suprised that it isn't optional already considering it's a little too "in your face" for a feature that can't be disabled. I understand the reasoning for it, but mIRC has scripting that can be used to split messages and the newer versions have an option to split messages, so why should people who use those options have to listen to an unnecessary warning beep?
If nothing else, just disable the beep if you have mIRC's split long message option enabled. That doesn't help the people using custom cut scripts, but it does make sense for people using mIRC's built-in feature. If mIRC knows it's going to split the lines, why warn someone about a long line?