what you mean by
searching php pages that use server side includes
are you searching through parsed pages? Because if so, you should be able to read the content of the include files too, as they've been parsed through the server, hence are part of the page.
If you're searching through raw code, then within your serach, you can search for the include string, if found extract the include file's name, then search that. (Sounds like a headache).. You'd be doing this with regular expressions, I guess.
HTH
Kamy