What is the DocumentRoot in your Apache config (for this VirtualHost, if you are running several)? Also, if you bump the LogLevel up, the reason for the 404 will appear in the error log so you could then stop guessing and actually know what the cause is.

I've made a symlink to /var/mirrors/minicpan from /var/www/public/minicpan. Does this seem like a sane setup?

It's not utterly insane. But Aliases are generally preferred to symlinks if the link is just there to allow the webserver to serve content.