My theory is that when you die and become a Force Spirit, you regain the powers you had when you were at your strongest. Yoda was once extremely strong in the force, but by the time of the prequels he was old and weaker. Perhaps there was a point when Yoda was younger where he was powerful enough to affect the weather.
However, Yoda is not the type who would abuse his powers to kill someone. Doing something like that might throw the Force out of balance and prevent him from becoming a Force Spirit any longer, since only light side force users can become force spirits.
only 4 known Jedi have ever become a force spirit after they die Qui Gon Jinn, Obi Wan, Yoda and Anakin and I doubt that Yoda could manipulate weather when he was alive no matter how strong he was in the Force.
Nothing is impossible now, especially after seeing how Leia used the Force.