Our business mostly customizes X-cart, Magento and PinnacleCart. We have had great success with both X-cart and Magento for SEO. We haven't had much experience yet with PinnacleCart and SEO. We've only done customizations and modifications to that one so far, so I can't comment on how good it is for SEO.
Recently we switched most of an old CGI cart to X-cart (we still have to use the CGI cart for the checkout for now and some other parts, long story) and the number of google links went from around 680,000 to over 2 million and it's still growing.
The main thing you want to look for is how modern the html coding is behind the shopping cart, do they use html and CSS elements appropriately, and do they use canonical tags appropriately. If the answer is yes, then it can be likely molded to work for you for SEO.
I hope that's helpful.