It is not strictly true that water is non-compressible. Liquids are about as compressible as solids, which is to say hardly at all by comparison with gases. But they still compress a bit. If you suddenly expose the water in a torpedo tube to 100atm, you exert that pressure on the water inside and thus on the walls of the tube as well. The water will compress a tiny bit and the walls of the tube will stretch and expand a tiny bit as well. (Because it is only a tiny bit, very little work is done, so there will be very little stored energy in the compressed and stretched materials.)
Water hammer is a shockwave caused by abruptly blocking the path of a moving mass of water, thereby causing rapid change in momentum. This change of momentum requires a certain impulse (F x t) and because t is so small (because it happens fast), F has to be great. So that means water hammer creates large forces and hence pressures - a pressure wave.
When you open a torpedo tube that is full of water, you do not have this, because the water on both sides of the opening is static and no change of momentum occurs. So it won't cause water hammer, just a bit of stretching of the walls of the tube.
As for the equalising valve, I suspect that will be because when you flood a torpedo tube in practice you most certainly do have trapped air, which will compress to 1% of its volume, storing a lot of energy and causing water to flood in as it is compressed - with momentum. So there can be large forces and energies created in that scenario, which you do not want for safety reasons. So you flood it progressively rather than instantaneously.
At least, that would be my best guess as to what is going on.