... and no, calibre can't read the subfolders and use them to assign tags to the books. Calibre can only read and store information in the filenames, not in the paths.
One way to handle this could be to make a copy of all the books using a batch file, and adding the "subject" of the book to the title/filename of the book. You would have to make the batch file yourself, perhaps from a file listing you import to LibreOffice Calc, and then export to a text file.
Exactly how to do this depends on your OS, the directory structure and the current naming standard of the books. It can get messy.
Perhaps: author - title - subject.format
Then when the books are added to calibre you can read the subject of the book from the filename, along with title and author, and use this to create a hierarchical view of the calibre library, ordered by subject.
Also see this part of the Really Fine Manual:
http://manual.calibre-ebook.com/sub_groups.html