Google Webmasters blog posted their presentation of SMX London, explaining about site architecture and traffic drops issues.

-Duplicate content causes drops in traffic: unless this duplication is intended to manipulate Google and/or users, the duplication is not a violation of Webmaster Guidelines.
-Affiliate programs cause drops in traffic: Affiliate sites with little or no original and compelling content are not likely to rank well in Google search results, but including affiliate links within the context of original and compelling content isn't in itself the sort of thing that leads to traffic drops.

More info: Webmaster Central Blog