If someone has manually uploaded to the directory, there is no way in which to know this.
When an item is deleted on the community, its deleted at that point if its not being used on any other resource. For example, if you delete a topic with images, those images are deleted if they have not been attached elsewhere using the "Use existing attachment" function.
The reason I ask if these are older files, is there were bugs a long long while ago where these were not being removed effectively