Would it be possible to implement a secondary server for the clouds and such? Or would that still cause latency issues.
The problem isn't server related. It is FE related. All of the rendering is done locally on your machine and anything of a tactical nature should be present on every player's local system and that means clouds would not be something that could be turned off. In turn, that means the limitation we are faced with is what the lowest end supported systems can do.
In a single player game it doesn't matter if the clouds are too much of a burden as they can just be turned off and the only player affected is the one with the low end system. In a multiplayer combat game turning them off would provide an advantage due to improved frame rates and due to being able to see enemies who thought they were hidden. That results in even people with powerful systems that could display the clouds turning them off so as not to be at a competitive disadvantage.
One solution is to have pretty clouds on high end systems and poorer quality clouds for lower end systems that block out the exact same sections of sky. Getting them exactly the same might be a challenge, I don't know.
