Zeta potential refers to the electrical potential at the interface between the particle plus all adsorbed matter (ions, polymers etc) and the surrounding liquid. When measured via electrophoresis, it represents the movement of the particle plus adsorbed matter in the liquid due to the electric field. It does not account for the screening of the "true" particle charge by the adsorbed material and/or the presence of electrolyte between particles.
Two simple cases illustrate this:
1. An ideal case where there is no adsorbed material and the particles are in high salt concentration fluid - the salt screens the interparticle electrostatic forces such that particles are not affected by each other. At low salt concentration the particles may be affected. The same zeta potential may exist in each case.
2. A case where a non-ionic high molecular weight polymer is adsorbed on the particles - the location of the interface mentioned above is now further away from the particle surface and so the zeta potential will be less than at the surface of the particle due to the decay.
Of course, you could assume an ideal situation in which case you could estimate the charge on each particle via electrokinetic theory but the uncertainties associated with the real world would be high.