The power of a shield reactor’s recharge is measured in Watts (W).
Each shield type in X3 (e.g. 1MJ Shield) requires a certain amount of reactor power to recharge it in a certain time. The relationship between the shield reactor power and the installed shield type power usage determines how quickly a ship’s shields will recharge.
Installing a smaller shield on a ship will result in it recharging to capacity faster than a larger shield would take to reach capacity on the same ship. Ships with higher rated shield reactors (more W) will recharge a specific shield type faster than a similar ship which has a lower rated shield reactor.
This means that two similar class ships, both with the same shield load out (e.g. 2 x 25MJ Shields), may have different performance in maintaining shields in combat if one has a more powerful shield reactor.
The choice of which ship has better shielding goes beyond just how many shields it can mount of a specific type.
NB: Shields do not have to reach zero before they recharge.