If used correctly then the answer is ‘no’, you should have no trouble using server side scripting languages such as ASP, PHP or Perl and still be able to have an effective SEO campaign.
Most dynamic websites use either a MYSql or Access database to store content and then dynamically pull content based on query string ids or sessions, which, in some cases, can cause duplication and SEO unfriendly URL structures. However with the search engine algorithms getting more complex, other factors are taken into consideration such as page load times, while size can also be a contributing factor.
For the most part, server side scripting languages are pretty clean in producing the resulting HTML; however I have come across many sites that loop through database tables and produce code cloning, which can cause issues with page load times. Sites with messy unnecessary code will have high code to content ratios and can potentially cause issues with search engines indexing your site and causing a loss in rankings.
Most of these issues are not so major that will cause your site to drop off the face of the earth, but it’s certainly something to be aware of and fixed if possible.
Adam Wood
ASP / SEO Programmer