I just recently wrote a document for doing SEO on ecommerce websites. I was hoping some of the forum community could take a look and leave me some comments Thanks! http://www.bloggleme.com/search-engine-optimization/seo-for-e-commerce-and-online-stores/
the tips are generic for the SEO. But keep in mind that not all of the ecommerce CMS are able to handle the things you are suggesting in the guide.
Anghus, Any quality ecommerce CMS should give you the ability to change those settings. Otherwise, you need to find a different eccommerce system. Personally, I have been using Magento Commerce. The SEO implementation is fantastic - however, the system is a tad bit slow.
I've been using zen cart now for a couple of years and have had no problems with SEO - in fact, I've found it really good for SEO and almost all my pages are well indexed by Google. I think you only have a problem with SEO an ecommerce platforms if they generate pages on the fly and that generally they are very good. Cheers Jason