Let's examine and answer each of your questions as follows.
- Does the density of the medium that is disturbed by a rigid body collision have any effect on the frequency distribution of the sound waves that are generated? For example, does the higher "stiffness" of the cage of water molecules surrounding the stones that are vibrating mean higher frequency normal-modes?
The frequency of the sound generated depends on the sound source and medium, the stones colliding in the air vs the water. Sound from the stones colliding in the water will have a higher frequency then the stones colliding in the air as deduced by observing a higher pitch. The pitch of a sound (how high the note is) depends on the frequency of the wave. The higher the frequency, the higher the pitch. Since the pitch heard was higher it follows that the frequency from the stones colliding in the water has to be greater. And yes since the stones resonant frequency(s) does not change in either medium the higher frequency cage or greater density of the water surrounding the stones must account for the higher frequency normal-mode of the wave generated. {It was logically deduced since the resonant frequency of the stones colliding will be a constant in both mediums. It then follows only one variable remains and it must not be a constant the main characteristic of the medium as it pertains to sound waves, its density and propensity to change shape, water is much more rigid and denser than air.
- Is this because it takes more energy for the sound waves to travel through water than through air, so that the ones that we hear from outside are the ones that had higher frequencies after the collision to begin with?
It does take more energy to create a sound wave in water than in air due to their different densities, water being more dense and stiffer so to speak. However the energy in this case should not have an impact since the amount of energy to cause the collision of the two stones in either medium would need to be constant for this comparison to make sense. If it were not the sound generated would just be louder due to the greater energy. Additionally adding energy to a sound wave will not effect its velocity, the energy only impacts its amplitude so all waves in water will travel at the same speed even if they have different frequencies and amplitudes. The higher amplitude wave will be louder.
- Finally, does the refraction at the water-air interface play any role?
Sound in air
In a gas like air, the particles are generally far apart so they travel further before they bump into one another. There is not much resistance to movement so it doesn’t take much to start a wave, but it won’t travel as fast.
Sound in water
In water, the particles are much closer together, and they can quickly transmit vibration energy from one particle to the next. This means that the sound wave travels over four times faster than it would in air, but it takes a lot of energy to start the vibration. A faint sound in air wouldn’t be transmitted in water as the wave wouldn’t have enough energy to force the water particles to move.
Wavelength is given by:
λ = v / f
where v is the velocity and f is the frequency. Since the frequency of the wave generated by the stones colliding in the water {at a 1 meter depth} is the same in both media, the wavelength will simply be proportional to the velocity of the wave. When the sound leaves the water the speed and wavelength both change. The sound wave will slow down in the air since the density of air is less than the water and the wave length will be shorter since the the velocity has slowed. But the frequency will not change therefore we must conclude that refraction does not effect the pitch of the sound one hears.