That's correct Vindex. Basically you can think of it as being similar to the effect of light passing through a prism.
However, it's probably more accurate to say the sound 'can' be distorted, rather than it 'will' be distorted. How much the distortion will be depends on the temperature variance, as well as other factors such as the salinity of the water. In SH4, the effect is perhaps a little too guaranteed, but all the same, it's nice that the effect is now actually in Silent Hunter.
If you want to read up on thermal layers, there's quite a bit about it on the sub Command and Dangerous Waters subsim forums, since thermal layers feature heavily in those two sims.
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