The effect of structural irregularities in photonic crystal fibers on scalar and vector modulational instability (MI) processes is studied by numerical simulations and experiments. For an anomalous-dispersion regime pump, variations in core ellipticity as small as 0.5% over length scales of the order of several meters are shown to have a negligible effect on scalar MI, yet they completely suppress vector MI. In contrast, for a normal-dispersion regime pump, vector MI is shown to be robust against such fluctuations.