As of today, the hardware isn't selling for less than the price of manufacturing it.
http://www.nintendoworldreport.com/news/31154
Nintendo is no longer selling the Nintendo 3DS for below manufacturing cost starting July 25, according to the company's first quarter financial results.
Nintendo began selling the hardware at a loss following the drastic price cut the system received last fall. Nintendo did not specify how much they were losing per hardware unit.
I feel like Nintendo wouldn't have gone out of their way to say they aren't selling at a loss if they were still selling at a loss in some way.