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A hierarchical model of microstructure of cometary dust seems to accurately capture the morphological complexity of these particles as observed by the Rosetta mission to the 67P/Churyumov–Gerasimenko. The main aim of this work is to investigate how uncertainties in the knowledge of the microstructure of the surface layer affect our estimates of gas production. New models that incorporate scale of inhomogenieties in a sound theoretical framework are used for hierarchical dust layers. The studied layers are constructed in two steps: first we design ballistic aggregates as the building units and then, using these porous blocks, assemble the layers constrained by the known porosity range. The mean pore size and permeability are studied. Modelling is performed for various values of porosity, grain size, and layer thickness. The simulation results are embedded in the thermal model, explicitly including a radiation thermal conductivity and a resistance of the dust layer for the gas flow. It is shown that the average pore size is satisfactorily approximated by a linear function of the ratio of the effective porosity of the layer to the degree of filling. Simple fittings were obtained for the layer permeability. Our results indicate that in the expected range of nucleus porosity, the gas production rate is weakly dependent on the detailed layer microstructure, and appropriate effective values of homogeneous dust layers can be used to evaluate the gas activity. We also note that adding complex elements into the model yields unavoidable statistical uncertainties within several tens of per cent. [ABSTRACT FROM AUTHOR]