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Not sure what is going on, but it seems clear that the nook is copying books from the SD card to main memory. I am not sure why it would do such a thing, but that is the only reasonable explanation.
CC will write exactly one copy of a file to the folder specified in its setup. Because the setup is done in CC on a format-by-format basis, there is no reason to make any distinction in CC between "Main", "Card A", and "Card B". The entire device, including SD cards, is considered "Main".
Calibre also will write exactly one copy. IIRC you can tell it to use a different folder "prefix" per format. These prefixes are added to the main/cardA etc when the file is written to the device.
My guess is that the built-in reader app doesn't like SD cards, so is copying part of all of the books to main memory so it can open them. This is, of course, a total guess. Perhaps someone else with a B&N device can provide more detail.
Aldiko always imports books into its own folders, which is why you are seeing two copies for books it is asked to open. The only way to avoid this is not to use Aldiko.
Moon+ will not do an import unless you ask it to, which I never do because I see no reason to use Moon+'s library manager. It does create some temporary files that it uses while you are reading the book.
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