Hi,
it all depends on what `AcousticSpeed(depth1 - depth2)` does (Aqua-Sim NG is not part of the "core" ns-3, so I can't be sure). However, the problem is that acoustic waves travel differently than electromagnetic waves. Well, also this is not entirely true.
Ok, let's start from the beginning. Any wave is affected by the medium it does travel into. It's not like the fake Ether idea, mind. The point is that a change in the medium density can introduce delays, reflections, scattering, etc. Common (visible) phenomena range from the light in the air/water interface (if you ever did look at someone in the pool, their submerged part of the body looks... strange).
For EM we have the tropospheric scattering, and for light we uses this concept in optical fiber cables.
For water, the salinity plays a crucial role in waves propagation, and two layers water might have a completely different salinity, like rivers inside the water. Go to the beach and try yourself - you might not feel the difference in salt, but you might feel the temperature shifts.
Hence, a way to make things more realistic in the simulation is to simulate also the presence of these effects.
Interesting enough, this might mean that two physically close nodes sitting at different depths can have a very bad channel compared to two nodes further apart but at the same depth ¯\_(ツ)_/¯