No idea, I've been avoiding even getting into those, so I take the negative score. I tried one do one of those but the mission itself takes MUCH time to do, and as you said, reaction fire kills everything it moves
I just registered myself minutes ago to check for some tips on this type of missions, and also those ninja base invasions. Probably I'm missing something (minmaxing production/money, research, whatever).
In M2.2, it gets to a point when ninjas are insanely OP and either you can't hide your bases, or defend them properly. In difficulty 2.