In this note, we apply the theory of stochastic homogenization to find the asymptotic behavior of the solution of a set of Smoluchowski's coagulation-diffusion equations with non-homogeneous Neumann boundary conditions. This system is meant to model the aggregation and diffusion of $β$-amyloid peptide (A$β$) in the cerebral tissue, a process associated with the development of Alzheimer's disease. In contrast to the approach used in our previous works, in the present paper we account for the non-periodicity of the cellular structure of the brain by assuming a stochastic model for the spatial distribution of neurons. Further, we consider non-periodic random diffusion coefficients for the amyloid aggregates and a random production of A$β$ in the monomeric form at the level of neuronal membranes.