I think, although I could be wrong that calibre directory structure is largely the way it is because of the conversion capabilities. A file structure was chosen so that book files could be grouped together, and easily differentiated between if there were multiple copies of the same title/author etc. Maybe it is not what I would have used, but it seems to be pretty compact and accessible if one really wants to access it in different ways. And the guy who wrote the program gets to choose.
BTW my calibre library has never been in My Documents folder. It defaulted to C:\calibre I beleive. But it can be anywhere in your file system you want it to be.