Can we ensure the security of a crypto-algorithm and -implementaton against acoustic cryptanalysis?
The problem is a very old one going back at least as far as the late 1940's early 1950's and has been shown to exist with Quantum Key Exchange as well.

You need to think of it in terms of entropy down to heat pollution where a coherent signal energy steps down due to inefficiency via various transducers to what is basically thermal noise where the noise threshold is significantly above any residual coherent signal.

Most people incorrectly think that TEMPEST is all about EM energy, it's not. It's about any energy (EM, acoustic/mechanical conducted or radiated even gravity) in one or more Shannon channels which have bandwidth, noise and propagation delay giving rise to phase as well as amplitude effects. It's also about transducers which can be bidirectional (a DC Motor/Generator being such a beast, as are some types of microphone/speaker by moving coil or piezo effects).

Put simply, a capacitor is two metal plates with an insulated gap. When current flows into the plates a magnetic field is generated that will cause the plates to move fractionally in sympathy with the current. Also some insulators are dielectrics which have a piezo effect as the voltage rises the dielectric deforms mechanically. Both of these effects will cause the capacitors to emit sound. Likewise inductance effects designers of RF oscillators are well aware that mechanical vibration of the inductive component will cause the resulting output of the oscillator to be modulated, it's frequently called microphonics.

These basic physical effects cannot be prevented only reduced or mitigated. In EmSec you look to reduce the bandwidth of any signal path such that it is less than the information bandwidth and also at signal containment/absorption.

Theses mitigations when done properly all add significant cost to a product. Therefor in a price sensitive market such as PC manufacture anything that is not regulated will cause a race for the bottom. And even where there are regulations (EMC) the market will still look at avoidance rather than meeting the intent of the regulations. One such avoidance is "direct sequence spreading" of the PC master clocks/oscillators such that the energy in a spur/sprog is spread so that it's energy/Hz decreases and thus meets the regulatory masks. Unfortunately the energy is still there and still caries the signal information and only needs de-spreading to recover the signal information. 

One solution to "singing caps" is high melt temperature wax or some hot melt glues they absorb the audio signals and reduce the effective channel bandwidth. Another partial solutions is 'sound absorbing foam' that also lets air flow through and the right selection of materials will significantly reduce the audio channel through fan and ventilation grills.

But as I noted all steps are "mitigations" not real "solutions", but may well be sufficiently effective in their own right if (and only if) implemented correctly.