Whether the shortages are intentional or not, Nintendo actually benefits here through the psychological principal of scarcity. People always, ALWAYS want what they can't have, and always DESIRE something they have to work very hard to get. Basic but proven, set-in-stone principles of psychology. So by demand being limited, they've (again, whether it's intentional or not is irrelevant) created an excitement and desirability for the product. Honestly I think it will benefit them in the long run with higher lifetime sales because it keeps people talking about the system for a very long time.
People talking about your product = strong word of mouth = more people talking about your product = massive sales multipliers.