In older versions, it wasn't hard to disable the default version reply. Khaled changed it so you couldn't easily disable it. So, I doubt he'll change it back.
Keep in mind that most people on IRC use mIRC, so it isn't like you are really hiding anything by hiding the version reply. I really don't see any reason to hide it.
-snippety snip-Moderator note: We don't help with changing the default version reply, as Khaled doesn't really like it.