I worked on the integration of ASPdotNet Stores to Marketworks (now ChannelAdvisor) and even though the pages are generated, they follow SEO best practices (Meta, Title, H1 and URL match). If you go into a store and click on an item you'll find that search engines will produce good product placement results. Of course, much still depends on the actual content of the page and the relevancy of data as presented - the more content that actually describes the item, the higher the placement (as long as there isn't any black-SEO practices going on).