I also run linux with ADE a Nook and calibre..
I have ADE running under Wine and no it will not see the nook as wine does not seem to read USB devices. But the nook works like a dream with calibre. I buy most of my books from B&N so no real problem for me.
But the books I do get, that I need to use ADE to allow the books to be "authenticated" ...well .. I strip the DRM from them and load those books into calibre. Only takes a couple of seconds.. extra.
I think that would be your best option
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