Actually, it doesn’t have to be either full pavement structure or a single hexagonal cell. You could model a Representative Volume Element (RVE) - a segment of the structure that represents its periodicity.
As an exercise, you can cut and paste this region around the pavement to see if it fits the whole pattern:
Research papers on hexagonal honeycombs (sometimes with various inclusions) will also give you an idea how to prepare such an RVE.
Once you have it, boundary conditions should be periodic (How to apply symmetry to honeycomb core unit cells - #2 by FEAnalyst) or at least try with regular symmetry first. For cuboid shape this will be easy.