The other way to handle this is to detect if cookies are turned on. You do this by writing a cookie and then immediately trying to read from it. If you cannot read from it then the client does not have cookies turned on and you can then turn tracking off. This has the benefit of working for all search engines, regardless if you know their user agent or not. However this also means that if a real person doesn't have cookies turned on they won't be tracked either.
The third way to handle this is to simply turn tracking off for everyone until someone logs in, tries to view their cart, and or adds a product to their cart. Since you will make it impossible for a search engine to do any one of those things this means that users will all have the functionality they need when they need it, and search engines will not be hindered.
PageRank is passed from page to page via links and the more links on a page the less each link gets. So if you have 5 links on a page and 4 go to pages that you want to have PageRank and one goes to a page that you don't want to have PageRank then you're sending 20% of the possible PR from that page to a place that doesn't need it. This is a problem.
These three issues are not unique to ecommerce sites, but they are very common with ecommerce sites. Once you address these issues you can work on SEO that is common for any type of site, such as increasing link popularity, using meaningful text links wherever possible for your internal navigation, adding keywords to your title and heading tags, and other things of that nature.