Version:           4.2.4 (KDE 4.2.4) (using 4.2.4 (KDE 4.2.4), Kubuntu packages)
Compiler:          cc
OS:                Linux (x86_64) release 2.6.28-11-generic

If you want to access a server via its IPv6 address (yep, this happens), the correct way is to put the IPv6 address in square brackets, like this:
  http://[2001:0DB8::1]:631/
The address above would access CUPS on the given IPv6 address (with a port you see why the brackets make sense).

This works.

But Konqueror will replace the address with
  http://2001:0DB8::1:631/
in the address bar and links.

This won't work.

Even without a port its not possible to access this server without the brackets, because Konqueror will throw you at file:///