That seems to have changed recently at least in the case of Google.
Googlebots, or the spiders that crawl web pages, are now reading Facebook comments on websites just like any other text content and the more interesting part is that you can also search the text of these comments using regular Google search.
To give you an example, here’s a comment from Robert Scoble that he has previously written on a TechCrunch page using the Facebook comments system.
..and here’s the same comment available through Google web search. You can in fact use search queries like “commenter name * commenter title” (for example – “Robert Scoble * Chief Learning Officer at Rackspace”) to discover all comments that he or she may have written on various websites that use the Facebook comments platform.
If you have so far avoided using Facebook comments on your Joomla website /blog just because of the SEO factor, you may want to reconsider your decision now, you can get this plugin free for your Joomla website here.
However I am not too sure if Google would pass any juice to any of the website links that some people may be dropping in your comments. Also, moderation of Facebook Comments is all the more important now as the comment text is part of the page content itself and you don’t want to be in violation of Google’s Webmaster Guidelines just because of those angry comments that do not use very civilized language.