[Alneyan]

After much testing, the explanation is actually not nearly as complicated as my first hypothesis: Shield Depleters simply do not take away partial damage, and merely remove the shields, hence allowing the attacking vessel to get two shots at the CA vessel, both dealing full damage.

So, you only need to hit them once with a Shield Depleter (after the CA cycle has begun) to break one CA, even if your weapon does not deal the required amount of damage per hit. Then you will need another hit of a Shield Depleter to break another CA, and so on until your weapon deals more damage than the CA can regenerate (where the Shield Depleter will no longer be needed).