I headcanon that the weather does sometimes respond to Nya's emotions, but in a way that kind of defies the stereotypical "rain means sad, sun means happy" pattern.
When Nya's happy, when there's an extra bounce in her step and she can't stop smiling, that's when it rains. Light and sweet to fill the world with that rich soil smell. The kind of rain that sends the whole world to glittering, and she can't resist twirling in it.
If she's mad? The sky goes as dry as the desert. Sure, her frustration can make rivers bubble up and currents switch directions, but her true fury shows by withholding rain from the ground. She's going to make people regret it and come begging for mercy.
Sadness, and especially grief, shows itself in thick clouds and a light mist. Everything is heavy and gloomy, but without the freedom of a full release- at least, not until she's ready to let it all out. Then it pours, rain dense enough to soak you with one drop, but there's something beautiful about that too- that acknowledgment of pain.
And of course, it often storms whenever she and Jay are together. While searching for him across the Merged Lands, Nya would often hear faint rumbles of thunder or catch distant flashes of lightning. She'd rush off in their direction- only to just miss Rogue without realizing he'd been there moments before her. During their tournament battle, a heavy storm had brewed, only to abruptly disperse when she won. And Nya thought she was constantly hearing distant thunder while Jay stayed with them at the monastery and helped search for Arin's parents, even if it never amounted to anything.
But when they finally got back together and Jay's memories returned? The Administration experienced some most unauthorized weather during their first kiss.
