Fighters in waves doesn't do anything, unless in waves with bombers. Aside from the fact that if passing through blast markers or shot at the "wave" would be destroyed together, they work independently. ie. if the wave of two fighters hit a torpedo marker, only one would be removed.
In your case, if a wave of two fighters tried to take down a thunderhawk, it would roll its save - if passed, it would take down the first and remain to take down the second, then disappear. If failed, it would take 1 of the 2 down and the other woud remain in play.
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