In my mind, a "flop" is a product which has performed grossly under what its seller intended. Useful examples of this include Shenmue (Million+ sales notwithstanding) and Evan Almighty (Over $174 million at the box office).
In this case, Nintendo clearly expected the 3DS to do much, much better than it has. I'm a bit surprised that they're surprised, to be honest, but it seems clear to me that the 3DS' sales performance up to the price drop was drastic enough for them to hit the panic button. You said it yourself: there were too many unsold units still on the shelves.
This situation may change, mind you, and it's good that you're taking the long view on this one, but I do think it's fair to say that the 3DS has hitherto been a flop. Which, I should note, does not necessarily mean "doomed."