It was already known that protagonist Jin could influence the weather with his flute, which can cause quite a few nice snaps. However, Jin also influences the weather with his actions. As you use more Ghost skills, more storms will set in. In other words: if you fight your enemies from the shadows instead of face to face, it will storm Tsushima more often.
This is intended as a constant reminder of the dark path that Jin has taken: from honorable samurai to the dark Ghost of Tsushima. Of course you are encouraged to use the Ghost skills: at the beginning the samurai’s weapons are still sufficient, but as the game progresses the difficulty level increases to stimulate you to become the Ghost.
This is a twist on a mechanic from other Suckerpunch games like Infamous: Second Son, in which the story changed substantially as you went the dark way. In Ghost of Tsushima, there is no real distinction between good and evil, so Suckerpunch has made it clear in another way that you are not as honorable as you were at the beginning of the game.