this is quickly explained.
Boxcryptor Portable does not use a virtual drive and connects directly to your cloud provider.
The two folders your cloud provider are not named identically due to the filename encryption and thus may handle this and Boxcryptor Portable may as well in conclusion.
On Windows Boxcryptor uses a virtual drive that underlies the restrictions of Microsoft Windows.
And there it's not possible to have displayed two folders with the same name.
Outside the Boxcryptor drive, the names are not identically (again due to the filename encryption). Within the Boxcryptor drive the encrypted filename gets decrypted to the same name as the unencrypted folder. That's when Boxcryptor notifies you about a hidden file / folder because it may only display one.
I hope I have been able to clarify the matter.
Have a nice and safe weekend.