How long were the 3rd and 4th and 1's? A whole yard or inches? Perhaps they would sneak it in a 3rd/4th and inches, but a full yard is too long if the defense is stacking the lone of scrimmage. Its easy for you to say "they should be practicing it", but if you never go under center, some would say you're wasting time by practicing that. Remember that some teams even use shotgun when kneeling the ball. Again, you're not going to run formations that Lou ran or possibly other formations just for fourth and inches because you don't run stuff you don't know and some think its better to spend the practice time elsewhere. I'm mostly playing devil's advocate. I'm not sure if they would sneak on an inches to go situation.
Also, so what if they stopped a couple 3rd and 1's? That happens sometimes because of the playcall the other team happened to be in vs. the one ND happened to be in and happened to out execute. ND ran a slower developing counter play on 4th and 1 and got 3-4 yards...