Well, knowing what we know now about 9/11, I don't think that any armed citizen would hesitate to blast a couple of holes in a would-be hijacker. I'd rather inadvertently hit an innocent along with the hijacker as opposed to having him or her take control of the plane. One dead beats 200+ dead (not to mention 3000 dead) every time.
As for training, the shooting itself is inherently similar to any situation - watch your target and your backdrop, shoot fast and accurately. Practice is probably the bigger issue here as it goes against the grain to shoot near innocents. I would think that avoiding pulling the trigger is a higher priority than in a home invasion situation, but you've got to be prepared, physically and mentally to cap him if necessary.
I don't know, maybe I'm half rambling here, but I have discussed this with plenty of shooting friends and we are all basically of the same thought - the hijacker would be history.