Kaworu looks up obediently into the clouds, and continues looking at them for a second or two as though sincerely considering the matter of the weather. This is an entirely superficial behaviour, mind--Kaworu has never in his (extremely short) life had a single thought about the weather, and is in fact entirely incapable of forming an opinion on it. But the neighbour didn't tell him to think about the weather. He was told to look at it.

So he is.

Except then the spider-human asks for help, and he returns his attention to more earthly matters. (Though not to imply that the weather itself is not an essential function of the earth.)

He frowns slightly, brow furrowing in bemusement.

"What do you want me to do about it?"

Does he think this is still about the weather, or has he figured out Jowan's problem is the neighbour?

Yes.