In SH4 the thermal layer lowers the volume of the signal. Sound from the sub is quieter. Sonar returns a less distinct signal. It therefore shortens the effective range of active and passive sonar.
Even the US Navy can't work up a simulation of real sonar conditions. There are too many variables and not all of them are understood.
Playing with a simulator that allows you to shine a light beam through the air into water or from water into the air I've learned a few things.
When the beam passes from a less dense layer to a more dense layer, it doesn't reflect, it refracts. Warm water is less dense than the cold water underneath. So the sonar signal going down wouldn't reflect off the thermal layer. Depending on its angle, it would refract to some degree.
When sound is traveling from a more dense to a less dense layer, things are more complicated. There is a critical angle, depending on the density of the water. At that angle, typically a low one of about 20º or lower 100% of the sound is reflected down and none reaches the surface. But this low angle is quite a distance from your submarine and affects there and further away as the angle lessens.
Coming nearer the sub, the angle increases. As it does so, less of the sound is reflected and the rest proceeds to the surface. The SH4 thermal emulation reproduces that part of the ocean surface between the 100% reflection angle and right over the sub where the angle is 90º. In that range it does a good job of reproducing reality. Outside that range it is doubtful an escort would detect you anyway.
So the protection given by a thermal barrier is not complete, just as it was not complete in real life. Our impressions of how the thermal barrier should work are largely based on movies. They are just as accurate about sub warfare as Oliver Stone was about the Kennedy assassination.