Google says that dynamic webpages and rich multimedia(flash sites) are not picked up by robots
Certainly Flash pages which have no text content are not picked up by the search engines - there's nothing to index.
But in relation to Joomla, the pages are certainly indexed. In fact there are tools built into Joomla to help with SEO such as setting your meta keywords and descriptions for an article.
Also, Joomla can display SEF (search engine friendly) urls, so you can get
for example, instead of
YourDomain.com/index.php?option=com_content&view=article&id=11&Itemid=19
you get
YourDomain.com/my-web-page.html
A sitemap is also a good idea as well as putting hardlinks in the footer of your page (on just 1 page is sufficient). There is even an extension for Joomla to generate this.