currently Ispconfig3 does not offer way to change domain document root, so i configured our horde manually. firs of all, you need ip-adress other than those used by Isconfig. then, of course, certificates. after you have setted prerequisites, create vhost-config in /etc/apache2/sites-available/, make symlink to it to /etc/apache2/sites-enabled/ and restart apache.
you can look /etc/apache2/sites-available/default-ssl to help configuring vhost, make a copy of it and adjust values as Squirrelmail wants.