It just opens up another point of attack. But keep in mind that all your php files are opening a database connection, an exploit could cause trouble with it aswell.
Some things will just require it for storage, hell back in the day all my forum's data was stored in text files in a directory set to 777. If you need it by all means go ahead, just make sure the code has security in mind. Also storing such things above the webroot would be a good idea.
Hope that helps.