Matt Cutts of Google Tweeted yesterday that “Google can now execute
crawlers can now ‘read’ some dynamically generated content previously
hidden. Exactly how much of this content is unclear. However, he does
specifically mention the word comments rather than all
love nothing more than to include complex functionality into their web
design whilst maintaining search engine friendliness.
Since Google is also indexing Facebook and Twitter comments and I notice comments on the envato network turn up frequently in search results I don't believe you'll be penalised for having too many comments. But the article I linked to above does state:-
With Google crawling and indexing comments, moderation will become
more important than ever. Website owners and administrators should pay
close attention to their comment sections to ensure they aren’t in
violation of Google’s Webmaster Guidelines. Too many comments left for
trolling and spamming purposes will result in a negative PageRank,
while hate speech could result in blacklisting.
So best to have a read and keep a close eye on what people are saying on your site.