Would adding an amazon store on a sub-domain, and linking to it on the main site, affect the serps for the main www domain (dilute the main site's theme or anything?).
I would say that if the site is young and you do not have enough "trust" then you could be hit with a penalty. The reason I say this is because I was testing ebay pages and amazon astores with the site in my sig and ended up with the "minus 30 penalty". This happened 3 days ago. There is no way to be sure exactly what triggered the filter but within 10 days of adding an Ebay page and an iframe astore my domain was dumped. I did not saturate my pages with affiliate links. In my opinion it was not excessive but remember this is google so who knows. I removed the astore and the ebay page and that is all that has changed. Check the amazon affiliate forum for more discussion on the duplicate content issues. good luck