Via SH_Cmdr one can adjust the water conditions from opaque to clear. What effect does this have on the game?

Other than making it easier or harder for the player to see underwater, none that I know of.

Not only underwater, but more the above water looking. Doesn’t interfere in anyway with AI behavior.

Ah, you are right. It's in Stiebler's add-on for H.Sie's patch

I can confirm that thermal layers are at least crudely modelled via SH3 Commander by what is in the congfig files (for GWX). As far as I understand the bottom depth limit of the sensor is altered. Which means that, once you are below that, you escape detection. The following is an excerpt out of the Randomised Events.cfg file in the SH3 Commander\Cfg folder:

;----------------------------------------------------------------------------------THERMAL LAYERS
[0:data\Library\AI_Sensors.dat]
;Randomly adjusts active/passive listening device values to simulate the impact of thermal layers - by Hemisent
;Only MinHeight values are changed
ChooseFrom=10
RndMidPat=1

Thanks Pisces. I hadn't bothered to look yet.

Ok, but also no difference in visibility to aircraft, yes?

Planes beeing AIs...no problems.

Ok, thanks to you both!

Thermal layers...
Used first in SH1, with the US vs the Japanese in the Pacific.
Thing about the Pacific ocean is that it's the largest ocean on the planet, with the longest dwell time for the sun to heat everything up.
It is also at the same time where you can find both the most shallow, and ridiculously deep seas.
Thermal layers will generally appear in the Pacific in the areas where your fleet submarine will operate against Japanese shipping.
But the Atlantic is brutally cold, most of the time.
Especially the north Atlantic.
Uboats were typically found in the colder seas, at least at first, with the Baltic, (grids AO-AG)where the training was done, the North Sea, between the west coast of Germany, including at the AN and AF grids, the west coast of Scotland and England.
Getting out to deeper waters in the mid altantic, there really isn't anywhere to find warmer water.
The only conceivable place for thermal layers in SH3 would be in the Mediterranean off the eastern seaboard of the United States, from cape Hatteras down to the coast of Florida.
Of course, the Caribbean Sea is going to be much warmer, as the south coast of Africa, but Doenitz never really intended for the uboats to be deployed in those areas, so the colder north Atlantic with its general lack of thermal changes were what got modelled in the game.
If you play it out as they (the programmers) want you to, then you should pretty well never find a thermal layer anyway, so why bother including that extra bit of processing data to the game?
Sure realism is nice, but the decision to rely on submarine profile only was probably the best way to go.

From what I understood, the water doesn't need to be hot or cold, it just has to be heated by the sun. In fact, wouldn't the cold Atlantic water being heated by the sun create a thermal layer more easily that the already mild water of the Mediterranean?

The ocean never stays warm enough.
Thermal layers would be few and far between.
The Mediterranean also has a lot of salinity, and these layers (like sedimentary rock) of salt, can also provide some cover.
To find a layer of water colder or hotter than another, either the sun has to be strong in the area or its caused by ocean currents, like an atmospheric jet stream, providing a constant influx of water warmed by the sun from the Carribean, for example.
In the deep oceans, water is not just water.
The salinity and even plankton can cause disruption, but I assume, since I don't know and can't be bothered to look, the rates of variability and occurrence of potential thermal layer was too bulky to model properly.
The short answer (that works for me) is that the places where the type VII is intended for, just never warms up.

Strange; posted this awhile back but it never showed up.

Anyway, thermoclines are made of different temps of water; doesn't have to be warm vs. cold. Can be cold vs. colder, etc. too. At least that's the way I understand it.

In the game they're modeled via Sh3 Commander. One never knows if they even exist let alone where they are, just as the German's didn't.

So the safe bet is just to act as if they will not protect you. Plan for the worst, but hope for the best.

I don't even think about them. No point to.