To say that the energy of the water is mgh is a simplification. It's really 1/2 * h^2 * A * mass density. The water at the top has more energy than the water on the bottom. The energy in the water is square to the water level, but the amount of water is linear.
It's the same with a capacitor, the energy is square to the voltage, but the number of electrons is linear.
It works out to the same 50% because the analogy is just very good. Dividing over two barrels/capacitors means halving the potential level (amount of water/load doesn't change), which means 1/4 of the energy in each barrel.