The thing I discovered very quickly was that if you're building a fleet don't use any CIWS. You want gauss cannons with lots of fire controls. I lost a couple ships to missiles because even though I had the accuracy and number of shots to destroy every oncoming missile, I didn't have the fire controls to target more than a few of the salvos at once. So when 20 salvos came in I had loads of wasted shots and most of them got through.
On the other hand I have several big 100kt battleships designed for solo work, and they use CIWS exclusively since there's no point using normal gauss if you don't have multiple ships supporting each other on PD.
Hope that made sense, it's 6am.