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My advice will be to only pay for directory links that drive enough traffic to your website directly to get a proper ROI.
If you pay for a directory link only to gain position in the SERPs you will most probably not get any ROI.
If you get the link from a directory Google does not like because it is known to be selling links it could even hurt your rankings.
In short: Paid directory links are not good for SEO.
I would definitely recommend to keep your shopping cart out of the SERPs. I would not recommend to use nofollow to try to achieve this goal. In a recent video Google's head of webspam, Matt Cutts, explains why using nofollow only really works for external links. It is probably best to no-index shopping cart page your in robot.txt or in the HTML of the page itself.