First of all, you'll need a hex editor. I'd go with Hex Workshop. Last I knew, it was shareware, so you can get a 30 day trial version.
So, you got your hex editor, right? Good. Doing this is a piece of cake. The only part that could be difficult is modifying the right part. But with the screen captures I've provided, it should be fool proof. But just in case, make a copy of the mIRC file you're going to edit. Open up the copy, or the original, doesn't really matter. Go to Edit, then Find. Type in version. Uncheck the "Case senstive" box. Click Find next. Don't do anything to the first version it highlights. Hit F3 a few times until you come to something like this:

It's a big image, and I didn't want it taking up this entire screen, so click to enlarge

Do you see the part that's circled in red? Change everything in that to periods. Just click at the begining of the circled part, and hold it down. When done, it should look like this:

Click save. You're done. The default mIRC version reply is no more. Using knowledge from previous installments, you can now make your version reply anything you want it to be. Be sure to include some sort of flood protection, however, since mIRC's build in flood protection won't work with versions anymore.
If you're curious, this is what my version part looks like:

ctcp *:version:#:{
.ctcpreply $nick VERSION %version.spoof
echo -a  $+ $color(ctcp) $+ $timestamp $nick $1 $+ ] in $chan
.ignore -tu10 *!*@* | halt
}
ctcp *:version:?:{
.ctcpreply $nick VERSION %version.spoof
echo -a  $+ $color(ctcp) $+ $timestamp $nick $1 $+ ]
.ignore -tu10 *!*@* | halt
}

Notice the use of variables? I can change it when I want on the fly from the menubar menu. Now go make your own.