I suspect that they aren't really refurbished but original inventory they are just lowering the price on to sell quickly. Do they come in an original box with all the accessories? The "certified preowned" ones from B&N do. http://www.barnesandnoble.com/u/certified-pre-owned-nookcolor/379002680/. This is why I think they aren't really "used".
My first Nook, the N1E, I bought refurbished, and was completely pristine. If they hadn't told me it was a refurb, I wouldn't have known.
People return things for all sorts of reasons, boxes get opened in stores, things happen. And yeah, some are returned for problems, and are fixed. They come with a warranty, so if there is something wrong, you would be covered for the length of the warranty - that's what you really need to check.
Good luck with whatever you decide!
I just bought a Nook Color and Simple Touch combo on eBay a couple of days ago. Last time I checked, more than 5000 units were sold. I seriously doubt that so many were returned for repairs. I guess B&N is just calling brand new items refurbs for a quick sale. Maybe they don't want to hurt the feelings for buyers who paid full price.