Disabling the version reply does not prevent you being flooded with CTCP requests, it just stops mIRC from replying to it. This can be good and bad. While you won't get killed for flooding, someone may be CTCPing you and since mIRC isn't responding you will be unaware of the attack. I think the usermode (where available) is a better idea - being server-side it stops the attack before it reaches you.
Don't forget that 0% CTCP reply on connection can also lead to you being banned from some networks. Warbots rarely return a version reply and a security bot may simply assume that you are a hostile connection which is reasonable in my view.