The structure block GUI does not support structure names over 64 characters, including directories, despite such names being supported by the game.
Structures with long names can be loaded from disk, but cannot be saved to disk. This is because saving a structure to disk requires manual GUI access, which causes the structure name to be truncated to 64 characters.
The structure name field in both the SAVE and LOAD mode GUIs is limited to only 64 characters. We can use /blockdata to change the without having to access the GUI, which allows for names over 64 characters. However, the name will be truncated back down to 64 characters if we update the structure block via the GUI.
This appears to be an oversight because loading structures with a long name works just fine. We can test this by using /blockdata as mentioned (just be careful not to cause the structure name to be truncated) and then using redstone (such as a button) to load the structure.
On the other hand, we cannot save structures with long names to disk because in order to save a structure to disk we must manually press the save button in the GUI... which consequently causes the structure name to be truncated.
Overall this behaviour is inconsistent and makes dealing with long-named/deeply-nested structures troublesome.