A CD does about 200 damage. A battleship missile has about 100,000 hitpoints. All missiles explode on impact. It is not the CD explosion that detonates the missile, but the physical impact of the CD projectile. If it was immune to that, then it wouldn't explode when it hit its target.
A possible solution is making CDs work like cloak disruptors, but then CMs would become obsolete for countering CDs.
PS: Additionally, concerning BS Cerberuses. I spoke with Titan yesterday and he had a great idea which I asked him to post here, but apparently he forgot.
Two types of Cerberus turrets. One is for close engagements, identical to the one we already have, but doing 50K dps instead of 45, with other stats unchanged.
The other is a long range one. It is less energy efficient than the short range one, but it is slightly more efficient than primaries (for example, if prims did 0.28 damage per energy, these cerbs would do 0.3 or so). It should be faster than short range cerbs, but slower than primaries, while having a slightly greater range (3.5K). The refire is 1, or 0.75 in the Nomads' case.