Including files is never good for performance.
Besides which; just how more managable does extracting the queries make your code?
If you have to edit a query then yes you can just edit the sql file, but editing a query usually also means that the output changes and that therefore you also have to edit the PHP that handles the output.
A function lubrary or OOP may be a better solution. Then you can create self-contained functions to both execute the query and process the results.
Yes you'll have to edit PHP again, but everything that deals with the SQL is gathered inside one function which makes is very easy to manage.