I can confirm this behavior.
However, it has nothing to do with IPv6. mIRC is actually stopping at the [.
For example double clicking "http://www.example.com/test[foobar]" (which is a perfectly fine URL (just unencoded)) opens "http://www.example.com/test".
 should normally be encoded.
This is related to http://forums.mirc.com/ubbthreads.php/topics/238811/mIRC_can_t_handle_URLs_properl
IPv6 might need a special exception. It's well defined enough to not interfere with the current punctuation delimiters.