But they fire two shots at 50%, statistically one will hit and the chance for two is there while a system that fires one at 100% can only hit one.
You might be misunderstanding probability a bit, though, I don't think it's a bad thing that CIWS gets 50% chance to hit.
Going based on gauss cannon Rate Of Fire tech:
2 shots at 50% accuracy, without bonuses:
Have a 25 % chance to hit zero shots.
Have a 50 % chance to hit one shot.
Have a 25% chance to hit both shots.
1 shot at 100% accuracy, without bonuses or penalties:
100% chance to hit one shot.
That said, I still think CIWS should still exist as they are, specifically because I feel the military maintenance of a full sized gauss cannon is the cost of having such an accurate weapon system.