For a boost converter you can design one with idealised components and all the equations still make sense, voltages and currents remain finite. From these voltages and currents you get an efficiency of 100%.
A charge pump with zero simply cannot be analysed in this way Trying to do so results in absurd answers. What happens when you connect a perfect capacitor to a perfect voltage source through a perfect switch? Trying to calculate the current results in a divison by zero. The same problem applies to connecting two perfect capacitors.
Lets say we have a capacitor charged to a given voltage and connect it to a voltage source of a higher voltage via a resistor. Lets assume for now that we let it charge fully (ignoring for a moment that doing so would take infinite time). We find that changing the value of the resistor does not change the efficiency, the total energy drawn from the voltage source remains the same. The efficiency is however dependent on the ratio between the starting voltage of the capacitor and the voltage of the voltage source. A smaller voltage difference leads to a higher efficiency tending towards 100% as the voltage difference tends to zero.
In our charge pump there is not infinite charging/discharging time so resistance does affect efficiency but as resistance tends to zero efficiency (for a finite voltage difference) tends towards a finite number less than 100%.
The charge transferred on each switching cycle is related to the change in voltage on the capacitor by the capacitance. To transfer a finite average current to the load we either need to transfer a finite charge per cycle or we need to have an infinite number of cycles.
So making your 100% efficient charge pump would require either an infinitely big capacitor or an infinitely high switching frequency.