Will a 6 kW electric storage heater be costlier to operate than a 3 kW elecric storage heater?

No.  Fundamentally, their energy consumption is the same.  A  6 kW water heater will use more power while heating but will only operate half the time as a 3 kW water heater which has a slower recovery rate.  Given a volume of water, the amount of heat needed to raise its temperature to a desired temperature does not change.  Amount of heat = heating rate x heating time.  Therefore, a higher kilowatt heater will have a shorter heating time; a low kilowatt heater will have longer heating time.