Hi Tim,
Thank you for using sh404sef! We are working on a you moz post for Joomla 3 SEO. Your input is welcome.
We have a couple references regarding duplicate content & Joomla. (see below)
http://anything-digital.com/sh404sef/news/canonical-urls-and-joomla-seo.html
http://anything-digital.com/sh404sef/news/ranking-factor-dilution-and-joomla-seo.html
Thank you,
Jess