Superposition is valid in vacuum, well, actually, until the photons have enough energy to colide and form an electron-positron pair.
It's also valid in most transparent material, again, assuming
1) each photon has no enough energy for example to extract an electron form the material like in the photoelectric effect, or creating an electron and a hole in a semiconductor, or ...
2) there are not enough photons, so you can model the effect using linear equations
And there are weird materials where the non linear effects are easy to trigger.
The conclusion is that superposition is only a nice approximation in the easy case.
https://en.wikipedia.org/wiki/Nonlinear_optics :
> In nonlinear optics, the superposition principle no longer holds.[1][2][3]
But phonons are quantum waves in or through matter and the superposition principle holds with phonons AFAIU