Hi, I can only answer to the first question!
Do you use some mod/shader that adds more transparent water? Like Shallow waters shader? I know it's included in Zedi's test campaings, and also as an optional mod in Dynamic environment. The shader used there makes the bottom of the sea visible, but also keeps the sub visible even if it's 150 meters deep. Ofcourse in reality this shouldn't be possible.
Stock game has quite nice water transparency, the bad thing is that imported ships won't be visible under water when looked above the waterline.
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