First of all he could he wanted to, second he doesn't have to? The atmosphere was heavily affected by amertarasu on the ground when he first used kirin. So the water dome will also greatly affect it just in the opposite way.
Is any of water dome vaporizing in order to affect the atmosphere? Not unless a Katon jutsu is thrown at it. Does Amaterasu burn things thus causing smoke to enter the atmosphere changing it's temperature? Yes. And maybe Kisame can but he has no idea that Sasuke is even prepping an attack from the sky so it's a fat chance he just moves up that high especially since the lowest clouds sit around 2000 metres in altitude!
Plus Suigetsu is distracting Kisame so why would he randomly think, "oh hey, this guy is slashing his sword right at me I'm gonna fly 2000 m up into the air and then stay there for a non instantaneous duration so I can cool the atmosphere for whatsoever reason..." Doesn't make sense.
Now that I think about it, Chidori Spear is long enough to plunge into water dome and electrocute Kisame as electricity that's conducted keeps conducting until it reaches an insulating material. Killer Bee could never use Raiton in his fight against Kisame as he would be electrocuting himself cus he was in it.
