These are optical clocks, so their rates are in the hundreds of THz to PHz range (1.121 PHz in the case of the Al+ clock). A 1e-18 shift corresponds to a ~mHz f

These are optical clocks, so their rates are in the hundreds of THz to PHz range (1.121 PHz in the case of the Al+ clock). A 1e-18 shift corresponds to a ~mHz frequency deviation which a decent frequency counter can resolve in around 1s. However, no optical clock is actually that stable at short time scales, and the averaging is required to get rid of these fluctuations.