I don't know what created the "Books" folder on the N7. On my N7 I manually created a Books folder because that's where I put books copied from my PC, but I've never seen any software create the folder automatically.
The only way to deal with dodgy epub or mobi files is to open them to see what the book is, then manually rename the file. On your PC I recommend Adobe Digital Editions
for reading epubs. You can just double click the file and it will open, so its a lot easier for working through a disk full of epubs. There's no need to import it as you have to with Calibre. If you have the Kindle Reader installed it works the same way with obis: just double click the .mobi file and it will open.