I do not think most webservers will be set up with one IPv6 address per website. As is, most IPv6 enabled sites that share an IPv4 with another site and also share their IPv6 address with those same sites. Assigning one IPv6 address per site would add complexity for little benefit.
How long ago are we talking? Apache 1.3? That used to have a few nuances but it's now been superseded several times over. I didn't use 2.0 a whole lot but I don't recall it ever being an issue with 2.2 and we're onto yet another engine rewrite with version 2.4 (which has been available a few years now too).
