Amount of substance expressed in yoctomole units
Well, the closer you get to atomic detection limits, the less sense bulk units make, that is correct.

However, coming from lab scale units it is much easier to scale down directly with SI prefixes — the exact reason what they were designed for. Therefore, it makes sense that these papers might say ‘Our predecessors could only detect $\pu{10zmol}$, we have lowered the detection limit by a factor of $100$ to $\pu{0.1zmol}= \pu{100ymol}$.’ And that is basically what they say. I note that both abstracts immediately place a molecule count behind the amount in ymol, so they are well aware of the scale of their unit with respect to molecules.

Once you get to the full molecular scale, you will be dealing with a type of quantisation this way or that; whether you are reporting energy, charge, mass or amount. In none of the other cases is anything special described for atomic scales so why should we make an exception for moles? Just make sure that the value itself corresponds to a whole number of molecules within the boundaries of rounding errors.