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The best first line defence against planes might be missiles.
If you have missiles ready to respond the window of opportunity depends on finding some set of conditions where missiles cannot be used.
By the way, I am rather less sanguine about nuclear power than I was because it occurs to me that if we are prepared to let an unsupervised literature degreed green activist write the Climate Change Act (Bryony Worthington who was lent to the government by Friends of the Earth and now a Baroness) who, I wonder, will they get to direct our nuclear power policy and will they be looking to over protect us or make an "I told you so " situation?
PS I can't say I'm happy that the government (in the form of the MOD who are answerable to the government, in principle anyway)are going to allow our nuclear deterrent be looked after by a private sector company.
I guess our troops are too busy being sacked or sent to act as spectators at the olympics to look after any military hardware themselves....though it seems to me the MOD is very good at spending money on the wrong thinsg and then not letting to troops near any of it in case they want to use it.... such is life.
Dive bombing required special engineering. I suspect that special overrides would be involved in diving a fly by wire plane in the ground. Unless the concrete containment of the tertiary containment unit is really really badly done, it is going to beat the plane. Flying a plane which is safety factor limited against a building that is safety factor limited give much higher chance of success. The trade centers failed, not in their collapsing, but in not surviving just a little longer before collapsing. It is possible that had they continued using asbestos in the process instead of the slightly less capable material, it might have survived longer.
Building reactors underground isn't a Nuclear Engineers job, it is a Civil's worry.
Looking at the responses on the issue of planes flying into nuclear plants, it may be worth adding a few things to the thread.
As DaveE is suggesting, there have been studies carried out which have concluded that nuclear plants can withstand impact by airliners. This link gives an example of a US study carried out in 2002 which considered impact by a Boeing 767:
Note that the validation status of structural impact computer models is way above that of the computer models we normally talk about in this forum, namely climate models. The Greenies only accept computer models which give politically correct results. so they would reject any computer model which demonstrates nuclear safety, whilst at the same time accepting the far more dubious climate models as being settled science.
Brad's point that an aircraft is pretty flimsy in comparison with a nuclear plant concrete outer wall is illustrated with this Youtube video clip (narrated by Carol Vorderman), which shows an F4 Phantom disintegrating when it hits a concrete wall:
One point that could be made regarding a repeat of a 9/11 incident in the future is that the 'easier' route to gaining control of a plane, by hi-jacking the plane, is effectively now closed down. It is now much more difficult to smuggle weapons on to a plane due to increased security at many airports and the cockpit area of airliners is now effectively sealed off. Also the attitude of airline crews and passengers to being hi-jacked is substantially different following 9/11. Before 9/11 it made sense to co-operate with a hi-jacking and treat it as being a bit like an armed robbery; after 9/11 it makes a lot of sense to attempt to mob and overpower the hi-jackers if you think they intend to crash the plane or blow it up. So I think a future 9/11 incident would require a terrorist organisation to recruit an airline pilot for a suicide mission, or have some of their people train and get jobs as airline pilots to be used as 'sleeper agents'.
On JMW's suggestion that ant-aircraft weapons could be used to defend nuclear plants, I think the prefered practice is to send up military fighter jets to investigate any slightly suspicious behaviour by airliners, and the most likely targets in the UK are expected to be skyscrapers and landmark buildings in London rather than nuclear plants, which as Brad points out could be tricky to hit. Most countries accept the idea that it may be necessary to shoot an airliner down if it is seen as a significant threat, but there is one exception to this - Germany (where JamesV is resident). In Germany they did introduce a law that allowed commercial airliners to be shot down, but it was ruled as being unconstitutional as it contravened the human rights of the terrorists (there was a rumour that German greens were behind this ruling):
On underground nuclear plants, the idea does exist, but only for small scale plants of not more than a few tens of MW. Sweden built an underground nuclear plant called Ågesta about 50 years ago that was under a suburb in the capital city, Stockholm. There is a proposed modern day small scale reactor called "Hyperion", which supposedly has a hundred orders, which is intended to be buried underground. As I understand it, burying nuclear plants underground is regarded as too expensive for normal sized plants, and is probably not compatible with the fairly high water table that occurs at many sites.