Sorry for being late
Jimbuna, as I said, "StormConditions" has no effect since I have the stock game, no patches installed. But I've solved this problem by editing the weather in scene.dat file and checked the option to apply the weather from scene.dat file to any mission/career.
More questions incoming:
-If I have flooding in my submarine, the sub's flooding speed will be affected by its current propulsion speed? If I'm moving, the flood will move faster?
-When I'm returning to base from my patrol, the time to travel the distance between my location and the base location will count?