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We have a number of e-com stores and honestly I don't think it makes any difference, Google is pretty good at figuring out what are 'store' pages and what is actual content. If you don't want those links to pass link juice just no follow them although I think there was something a while ago about no longer needing to do that. Perhaps someone else can clarify that. Bottom line for me though would be to just design the site that makes the most sense to the customer and not worry about Google.

Google (matt Cutts) specifically talks about links on top hold more value than links on bottom. If you are concerned with those links on the top, I wouldn't IMO. Almost every major site including SEOMOZ places their links for login,register on the top right and their rankings are not touched.