Afaik, Mobipocket Desktop does not read subdirectories.
And with the last version, I can't even change the default directory to store books into (it resets at every start-up of the software).
I'd like to import my books keeping them in different subdirectories, but I can't. But that's another problem...
With this script I keep my books organized with Total Commander, and I use that same tool to synchronize the iLiad...