How do I delete empty DCIM folders from my iPhone?
If your iDevice is jailbroken you can install iFile from Cydia in that device and then you will be able to access the file system directly.

In /var/mobile/Media/DCIM there are empty folders that you mentioned. You can delete them manually (rmdir empty_folder_name).

You can do this by accessing the file system of your iDevice via SSH also.