Apple does not support viewing or manipulating the internal file structures on iOS devices, and doing anything on the device from a computer as you are doing can corrupt the Photos database. The folders are part of a database used to manage the content of the photos app. Each folder is a node in a database tree structure, designed so the Photos app can find content quickly. And there is nothing stupid about organizing data in a manner that simplifies management.
Here is the correct way to access and transfer photos from an iOS device to a computer→Copying personal photos and videos from iPhone, iPad, or iPod touch to your computer