No, that makes no difference. If your pages contain well formed html with any type of normal link, search engines will be able to read it.
What will break things for the SEO will be stuff like Javascript links and links in Flash; client-side stuff is what wrecks it for search engines.
Using absolute links will make your site a pain in the arse to develop because your links on your local dev site will go to the production server, making testing harder.
Mark