The mounting height is only used for calculating the correct transfer functions. The transfer functions are what is used to estimate wave energy (i.e. height) from wave related quantities such as pressure and velocity. This means that if you have an AWAC with AST operating properly, then it really is not that important. If the AST is not working then the wave estimates defaults to the combined pressure and velocity based estimates.
Naturally for PUV type of wave estimates, the mounting height become important so we get those transfer functions correct. This applies to the Aquadopp, Aquadopp Profiler, and Vector.