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First: A PHP file is parsed on the server end and goes to the end user as nothing but HTML. Take a look at a page that is done in php by clicking "view page source" in your browser. You won't see any PHP code because it all gets interpreted by the server and turned into whatever the developer wanted it to be.
Second: PHP has been out a LONG time. TONS of sites are driven by it, and many other languages. I certianly hope that the engineers are not so stupid that they can't program a crawler to go over a coded site.
The only thing that may be a hinderance is if you use a CMS (Content Management System) that doesn't link to things well.
and article URL looks better to an SE as /article/category/title as opposed to article.php?=a=146. Pretty much all CMS'es now support a good permalink structure.
I'm converting all my sites to TextPattern right now. Static HTML sucks.