You're probably right, I'm sure some do want to change it. The thing is, if it were done in a way to only just not reply, then someone could just script their own reply. So it would have to ignore/discard any incoming ctcp version requests. If the user wants block mIRC's version reply, then it's only fair that ALL version requests be ignored imo.
Update: An elegant method for stopping the version reply can be found
here.