As far as I know nothing like a thermal layer is moddeled into the game. However, I think Sh3 Commander does have the ability of adjusting (randomly) some depth hardcap that makes you undetectable by sound below some depth. So it sort of models a hard thermal layer. But far from realistic. (oops, I forgot I posted this in Sh4 section, never mind that)
Something else. Dr.Sid (a user of this forum) made a little simulation program to show how soundrays get bend around and reflected underwater based on a soundspeed profile.
http://www.subsim.com/radioroom/showthread.php?t=120487
You should know a bit about what soundlayers are and how hydroacoustics work to really make sense out of it. If you create an 'increasing soundspeed' curve just below the waterlevel, and a 'slowing down soundspeed' below some desired layerdepth you can indeed see that sound emitted above the layer stays there. And a sub right under the layer would hardly receive/perceive that sound. Load the "surface duct" sound profile through the SSP button and test different sound source depths (i.e. 10 m) You'll notice a pretty dark area under the layer, but not if you get too close. Then a DD could stil get a direct ping return path. Similarly the sound that you emit below the layer (sound source depth 110m) is alot fainter above it when far away. But if the DD is on top of you there also is a straight path. Soundlayers are not mirrors reflecting the sounds in the other direction. It depends on the angle if the sound penetrates it.