Maybe yes.

PHP pages *may* affect your site indexation, if not ranking at least.

There are a lot of bots that ignore pages that are dynamically generated.

So, the best way to counter this effect is to rewrite the URLs using either PHP or using a .htaccess file thru mod_rewrite (if running under Apache)

The sites that benefit from this, the best, are Forums. Where each and every page is dynamically generated.