I took time, since I can't control weather, but since now, there were few lightning storms and I didn't have any problems. All I did to fix that is (for some reason I have gateway moteino on 3.3v instead of 5v), to move moteinos supply from RPi from 3.3 to 5v.
So I guess this is solved for good, there was just not enough margin on 3.3v