Only in a good way. Even though ezimerchant version 5 websites will be dynamic, database driven sites, they will appear identical to the search engines after the initial upgrade. So there will be no negative SEO impact whatsoever. In fact, to the search engines it will appear to be the same static website, which is fantastic for SEO. ezimerchant websites have always ranked extremely well and will continue to do so.
You will have a few new SEO options in version 5 though. In version 4 it was impossible to control your URLs. Category pages were category1_1.htm and there was nothing you could do to change it. In version 5 it will be possible to change the page names to almost anything you like. We will even take care of making sure the search engines still find the old page and update to the new page without losing any of the SEO the old page had.