Summary: Many design elements work for Amazon.com mainly because of its status as the world's largest and most established e-commerce site. Normal sites should not copy Amazon's design.
That report is a decade old. While I'm not going to hold up Amazon as the ideal e-commerce design, the site has been drastically altered since 2005 and many of those complaints are invalid now.
http://www.nngroup.com/articles/amazon-no-e-commerce-role-mo...