And please, don't come back with "they hadn't thought of it at that time." We have no concept of what they had and hadn't considered at that time. They tried and failed with "a minimum response" the first time.
Part of me agrees with the "if they had them they would have used them" mindset, and of course, hype like this sells books. But, I remember in the months after Sept. 11, a lot of people were speculating about how soon the next attack would come. It seems to me that the events of Sept. 11 are still having the desired effect... people are still frightened, the "terror alerts" are still high... they are still getting a lot of mileage out of what they have already done. But, we are getting complacent. We are beginning to let our guard down in some places, and in other places it has become clear that we will not really raise our guard (i.e. the borders). Al qaeda can afford to wait, and in fact, gains by waiting. If the goal is simply the destruction of America, then getting nukes into major U.S. cities and detonating them in one swoop would seem logical... thus, the "if they had them they would have already used them" argument. But, if the goal is for certain elements to rise to power, to bring about a war that unifies all muslims in the world against non-muslims, then a bit more strategy would seem logical. Poking the sleeping giant America into swatting at cells of Muslim terrorists here and there was a first step, allowing the terrorists to carry the corpses of muslim children supposedly "murdered" by the U.S. in the streets as recruiting posters on al jazeera. Striking on 9/11 was another step, escalating the violence and the level of attention to "the cause". Arguably, the U.S. has responded exactly as the terrorists wanted us to... we have gone into predominantly Muslim countries, killed muslims, and "occupied" muslim lands. But, again, we have been unwilling to unleash the full force of our might, and we, as a country, have become more divided rather than more unified.
These are all just random thoughts, but it seems to be there in another side to the "if they had them they would have used them" argument... a certain strategical planning to unleashing of their terror attacks, depending on what their ultimate goal is, may be more effective in their minds.