This was a known issue introduced with the second sim update. It has gotten better, but it does still happen.
I’m guessing there’s a specific set of conditions that cause MSFS to generate thunder and lightning (and it’s not just where reported in real world). Once it’s triggered it seems to go completely overboard with the frequency. You don’t encounter it that often, but when you do - oh boy!
I last found this problem flying in equatorial Africa a couple of weeks ago. Only good news is that they seem to have improved the impact on performance … originally it was a complete stutterfest every time the lightening effects occurred. That is better now.
I just ignore it. Exactly like you wouldn’t in real aviation.
Lots and lots of debate about it last year…