During ingest, yes. During a drag-drop, that depends on what you are dragging and where you are dropping.
During ingest, there is the option to preserve source directories, and yes this works even if ingesting from a folder. (See attached)
If you drag a folder from somewhere in Photo Mechanic's navigator into some other location in the navigator, the subfolders are also maintained. In the other attached example, I dragged the "Test" folder from one location and dropped it on the "Downloads" folder and the subfolders were maintained. (In this example I was dragging from a removable drive, so the folder was copied and not merely moved.)