Actually, battery sizing is pretty simple. There is really only 4 variables and weight is not one of them (directly). Power, time, system losses, and a factor called Depth of Discharge (DOD) are the key players.
The size of a battery is measured in Watt Hours (how many hours it will provide a given amount of energy - Watts). Once that is established then comes the packaging and weight concerns. These are a function of the battery material technology and are related to the DOD factor I mentiond. NiCads wear out faster then Ni-MH by nearly a factor of 2, so a lot of weight is saved right there.
The real driver is the DOD value. To make a battery last for 100K miles it has to endure a lot of cycles. The greater the number of cycles the smaller the DOD value because you don't want to wear it out. Basically, lots of little changes in charge over many cycles (400h) vs great changes in charge for relativly few cycles (say, I donno, disposable camera). Small values for DOD drive up the W-hr size of the battery and, by extension, the weight.
So, long story short, the 400h IS carring around a lot more battery than it needs on any given day, but it has to carry that much so that you won't be in for a new battery every oil change.
Now changing a much smaller battery every oil change would be a viable scenario and would reduce the vehicle weight, but I'm sure the minds at Toyota decided that even if it was economically workable, the customer would not accept it from a reliability point of view.