I never actually thought of the tracking ramifications before, but occasionally I work with sites that have both the www. and non-www. versions of the site live. Does this interfere with tracking in Google Analytics? (i.e. would I see double stats if someone visited domain.com/product/ and another user visted www.domain.com/product/) As a side note, I know that you can now verify Google Webmaster Tools via Analytics if you already have it implemented, and you can set the preferred domain to either www. or non-www. in Google Webmaster Tools. So...maybe that takes care of it?
Visitors are tracked by page so you will see how many people visited /thispage whatever the hostname.
I always set up separate profiles with different filters. One records accesses to www on the correct hostname and another records all other accesses elsewhere. This second profile records visits to non-www, to Google cache, and scraped and copied pages.