Wild bunnies grow up with the wind and even if they haven't encountered it directly they've a whole colony of other bunnies to take their cues from
Try playing a radio quietly on some nights, not just windy ones but now and then, and then when it's windy you can pop the radio on and it will make the wind noises less startling. Making sure bunnies have lots of cover is good too, you could try some extra cardboard boxes for distraction and hiding in.
And absolutely don't teach your rabbits that thumping means cuddle time :lol: