i tried some cruiser missiles out tonight on a juggernaut. i pulled up to 5k and began launching at the BS. i could see the ship shooting at the missiles and since i didn't see the ships stats change i figured it was shooting them all down.
it was only after the fight that i learned that the BS hadn't shot down all the missiles and some had gotten through. i was surprised, because the BS's shield (from what i could see) didn't budge at all.
just coming out and saying "you shouldn't use them against shields" seems uninformed to me, the missiles are super slow. if you were to fire the missiles at about 3k, then the enemies shield would be back up before the missiles got there.
so from my experience, if anything under a BS class get within primary turret range of a BS they will die post haste. so the only alternative is to lob long range cap "torps" at the BS...but if they are practically useless against shields then you would be forced to get within the range of alternate weapons which in turn puts you right into the insta-death zone.
i believe something needs to be done to the cap missiles shield damaging abilities. i've not experienced how well they work against hull because i've yet to have one land against an unshielded hull.