Director of "Ghost of Tsushima", Nate Fox confirmed during an interview with GameSpot that the game's climate changes are really connected to the journey of protagonist Jin Sakai.
That is, if you choose to follow the path of the Phantom, you will have a darker scenario, with storms and lightning, while the honor of the Samurai brings a greater sense of peace and serenity.
However, it is worth remembering that there is a system in the game that also allows you to change that mood at any time, while using the protagonist's flute.
The game's plot follows the samurai Jin Sakai, who survives the invasion of the Mongol Empire on the island of Tsushima, Japan, who begins to cause terror and conquer territories. Your character will then need to put aside the samurai traditions to become a Ghost and guarantee victory.