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I'm not for sure how they go through the shields, but I do know that if you launch a missile at a starfighter and it hits them, they're toast. Larger ships like freighters and Star Destroyers have much more powerful shields and can actually withstand the blow. I know with Star Destroyers, and other capital vessels, the missiles do not penetrate the shields. They first have to be brought down.
I'm guessing with little ships the missile simultaneous overloads the shield and hits the ship. (same with proton torpedoes) _________________

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