In 3.3.10 the normal situation is that a file is stored by FileID, however there is still backward compatibility code for applications that used to run on version 2.5.2 or lower, where it does get the file by the ID of the file document object.
Normally you don't have to perform manual cleanups anyway, it will be a very rare situation where a file is still on disk but not in the database anymore, if nothing goes wrong they are just deleted together. Do you have a reason to assume you have unlinked files on disk?