I would be pretty surprised if any networks actually use this kind of a heuristic to ban clients. Certainly there are many legitimate clients out there with no such a timer, are they being banned? If this check is specifically targeted for a version reply containing mIRC, I see no problem in having these network admins modify their rules-- they would have to, and I'm sure they would.
That said, there is a good reason to re-enable the hardcoded flood check: the version reply cannot be halted via scripts, and /ignoring all CTCPs is not always warranted. Also I'm sure some users prefer to use their own scripts to manage an ignore list or flood control, so having mIRC at least have a sane default would help.
