Thank you for your replies.
Playing along with SH Commander I found that the water clarity thing was not its fault... in fact it does change clarity. It was the mod 16-atmosphere, it makes everything darker and this is something SHC can't fix. It's a little annoying to see the faces of your seamen darker than their hands for example, but not big deal.
About the weather system, I didn't know that speeding was bad for the weather thanks for that tip
Sometimes I get like 6 days with same weather, other times around 3. I'd say that 3-4 days of same weather is my mean.