Unfortunately, not all of the carts were investigated very well.
Zen Cart does not use Smarty. I've been using Zen Cart for about 2 years. Zen Cart's template system can be difficult to modify, but the upcoming version should rectify this. The best part about Zen Cart is the support from the developers and user community. It is stellar. There are several contributions that deal with the SEO issues.
osCommerce is the most popular freebie cart, but it is so riddled with problems that I would never use it. I call it 10 pounds of crap in a 5-pound sack. The support, other than the conflicting answers from the user community, is atrocious. It is not unusual to find hundreds of coding errors when an osCommerce page is run through the W3C validator. However, from an SEO perspective, it works fine.
I work on sites that use digiShop. If used conservatively (cart and checkout only), it does not create any SEO issues. My main business is SEO, so I look for these issues. I always add noindex meta tags to the actual cart and checkout pages because they hold no value for SEO. The digiShop code is pretty clean and easy to modify.
I have not used any of the others.
The main issue with SEO is with the home page and product pages. Product pages need to have customizable, spider friendly URLs, along with the ability to customize the HTML title tag and meta tags. The code needs to be clean. Many of the carts that I've looked at generate horribly bloated code that is riddled with errors.
"Democracy is two wolves and a lamb voting on what to have for lunch. Liberty is a well-armed lamb contesting the vote." -- Benjamin Franklin