Atomistic simulations are employed to study structural evolution of pore ensembles in binary glasses under periodic shear deformation with varied amplitude. The consideration is given to porous systems in the limit of low porosity. The initial ensembles of pores are comprised of multiple pores with small sizes, which are approximately normally distributed. As periodic loading proceeds, the ensembles evolve into configurations with a few large-scale pores and significantly reduced number of small pores. These structural changes are reflected in the skewed shapes of the pore-size distribution functions and the appearance of a distinct peak at large length scales after hundreds of shear cycles. Moreover, periodic shear causes substantial densification of solid domains in the porous systems. The structural evolution of pore ensembles is found to stem from the formation of shear-band like regions of enhanced particle mobility after a number of transient cycles. The spatial extent of increased mobility depends strongly on the strain amplitude. A scaling theory is developed to qualitatively describe the transformation of the pore initial configurations of small-size voids into larger-scale void agglomerates.