If you want CS:GO flashbangs for some reasons do them well - "counter" would be turning your (characters) head away...
Also, taking away piloting slot to counter this... So either this will be used so seldomly that nobody will use the counter or it will become a meta and everyone will be taking this. I don't think we want things to go this direction.
Also I think Muse have been telling us for a while that they don't want to implement something like this.... soo.... fruitful discussion is fruitful
So, just for the sake of humouring this idea, let's say that when the flashbang projectile hits the ship, it gives an audible cue and sticks to a particular location, when times up, it will detonate and cause whatever debilitating effects have been discussed. Counters would obviously be facing away from it and, perhaps to prevent audio disruption, moving away from it.
Even if you successfully counter the flashbang itself, you've still managed to somewhat disrupt the crew. Even so, I can just imagine five of these on a mobula for the most infuriating thing to play against ever conceived.
Also, the timer after the flashbang "sticks" to the enemy ship is shorter depending on range, rewarding skill. Then again, fast-paced brawls seem like the only possible area this kind of mechanic would make that much of a difference.
Humouring over. Please, do not implement guns that directly influence the crew's ability to perform specific jobs.
Maybe the minotaur could randomise your wasd keys for half a second after impact to simulate staggering :^)