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The PCI DSS is applicable to merchants and service providers, and not only to the ecommerce software they use. So that means that you have to audit the entire store (there are a lot of requirements that you can find on the PCI SSC website ), and not the single application.
For our part we are aware of it and will do our best on Magento to make PA-DSS facilitation happen.
I am aware that it does not just apply to shopping carts / web sites, but it is certainly part of it. My understanding is that these rules are getting stricter and fines are going to be steep for those that do not comply in the near future. If this is true it will kill off all the carts out there that do not pay attention to these details because merchants will be fined.