A unit's SEER2 rating is measured under controlled conditions at the equipment itself. It says nothing about what happens between the equipment and the register. Duct leakage subtracts delivered cooling without subtracting energy use, since the equipment still runs and still consumes electricity to produce air that never gets used.
In homes with ductwork routed through hot attics, leaked conditioned air is also frequently replaced by hot attic air pulled in through return-side leaks, adding load on top of the loss, both of which increase runtime and cost.