Does the ES need to measure the Capacitor charge voltage to ensure it does not exceed 3.0V, or does the cell count (2 * 1.5V) suffice, even if actual voltage may slightly exceed 3.0V?

No. the ES does not need to measure the Capacitor charge, it is inherently limited by the voltage of the two 1.5V nominal voltage batteries. That is why the rules require the charger to hold the batteries in such a way that nominal voltage can be read.