Why does PDF24 OCR creates to identical files?

This is because you have configured an output directory and you have checked the "Save in same folder" option. If the directory of the source file is the same as the output directory, the the app saves two files. The first save operation saves in the output directory and the second saves the result in the same folder of the source file. So, just use an output folder or "Save in same folder", but not both.