They were, yes, but that was only part of the problem. The plants we ponies grow for food need the energy of the sun to grow. Without it, they wither and die. And if the food died off, the ponies would have soon followed. Nightmare Moon, it seems, was too far gone to realize this, or so consumed with hate that it was what she wanted. I genuinely hope it was the former, but... there's no way to know for sure.