The phenomenon is called
Color Banding and in SH5 happens mostly at night when the range of colors in the sky is very limited - mostly blacks. The issue will be less or more visible depending on how much light there is in the scene (moon/clouds etc.) or HDR settings, but it will not go away. Also it depends on your graphics hardware and settings (how the gamma curve is set) and monitor.
Unfortunately, since the sky is procedurally generated from code and is not using a texture (like in SH4), no modding can fix it. The solution would have been to apply a dithering filter on the sky before it gets rendered and also apply a color correction filter to give more precision to the blacks instead of the whites (for this last one, some fixes could be done in the shaders).