Maybe the reason ctcp replies aren't ignored with /ignore -t is that they are NOTICE messages, not PRIVMSG, and according to the RFC, an automated client (bot) must not respond to NOTICEs. So, if client doesn't respond to notices (which means ctcpreplies too), there really isn't any problem. Besides, /ignore doesn't stop the messages from coming, it just hides them. So letting ctcpreplies pass through wouldn't affect a client in any different way than ignoring them.
The only difference is the display of the ctcpreply messages, of course. This (and only this) is where a /ignore switch for ctcpreplies would come in handy, although this is a minor issue because /ignore -
n already ignores ctcpreplies. Of course, there's always the scripted solution:
on ^*:ctcpreply:*: if $fulladdress isignore ctcp { halt }