There is absolutely no mention of ssl in /etc/apache/conf/apache.conf (or any other files in the same directory). At least for 1.2, there are the "ifdef ssl" entries and similar, but not so for 1.4rc1. Looks like a simple omission. Simple enough to add/fix, but it should probably be included by default.
Similarly for mod_perl it seems (it is checked for ini commonapache.conf, but it is never loaded in apache.conf).
when you install mod_ssl and mod_perl it says something like: Execute /var/db/pkg/net-www/mod_ssl-2.8.10/mod_ssl-2.8.10.ebuild config to have your apache.conf auto-updated for use with this module. You should then edit your /etc/conf.d/apache file to suit. then you edit /etc/conf.d/apache and add -DSSL to APACHE_OPTS and ssl works when you restart it