This was a workaround I found for the sun shining through the water.
Because the problem is due to the texture applied to the sun being rendered, the idea was to find a way to stop this from happening.
Please note, this does reduce the color effects to a degree during sunrise and sunset when the sun is below the horizon, but the colors are still very good.
If you are using any of the environmental mods, you will need to do this with each update you download.
First, get S3D also known as Silent 3ditor
Next. Make a backup of your scene.dat file. Now, open the scene.dat file with S3D. This is located in Silent Hunter 4/Data folder.
Refer to this drawing for the next couple of steps.
Go to 6: Node-Sky and expand that list (+) sign
Go to Parameter 13. Envsim. Expand EnvSim and then click on Properties. You'll see a list of parameters in the right box.
Scroll down to Sky[13] and expand that. This is where the entries are made.
Look at the following pictures for the next step.
Expand each entry unitl you find the entry where the sun is at -15 degrees. The reason I chose this is due to the disc of the sun being visible above above the horizon at -9 degrees.
Now change the SunRelativeSize value to 0
Do this for each entry below - 15 degrees.
Save the changes and play the game to test the results.
Additional notes:
Depending on the scene.dat file you are using (PE2, EE4, stock) you may need to tweak the SkyTextureIndex value and set it to ) sooner than the file has it.
You can do some fine tuing by changing the SunAltitudeAngle and moving the angles at -9 and -15. That's just personal preference.
Good luck