Oddly enough, i've found that i *can* fire missiles at shielded targets with proton tube equipped, but it only works at relatively short ranges.
Such as on the mission your video is on. When you're out that far it doesn't work, but when you're doing the close fly-by's at the end, missiles work fine.
Of course, this may not work for everyone, and in case it matters, i'm referring to the highest level version of that mission (empire side would be Clouds of Vondoru). But then again, on the easy version of that mission, you can just blaster the shield gens, so a non-issue there.
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That being said, this is still a problem, and a fix would be awesome.
Edit: it may just be that i was out of torpedoes, just checked it. Oh wells.