Charge transport within Coulomb blockade regime in two-dimensional nanoparticle arrays exhibits nonlinear I-V characteristics, where the level of nonlinearity strongly associates with the array's architecture. Here, we use different mathematical approaches to quantify collective behavior in the charge transport inside the sample and its relationship to the structural characteristics of the assembly and the presence of charge disorder. In particular, we simulate single-electron tunneling conduction in several assemblies with controlled variation of the structural components (branching, extended linear segments) that influence the local communication among the conducting paths between the electrodes. Furthermore, by applying the fractal analysis of time series of the number of tunnelings and the technique of algebraic topology, we unravel the temporal correlations and structure of the phase-space manifolds corresponding to the cooperative fluctuations of charge. By tracking the I-V curves in different assemblies together with the indicators of collective dynamics and topology of manifolds in the state space, we show that the increased I-V nonlinearity is fully consistent with the enhanced aggregate fluctuations and topological complexity of the participating states. The architecture that combines local branching and global topological disorder enables the creation of large drainage basins of nano-rivers leading to stronger cooperation effects. Also, by determining shifts in the topology and collective transport features, we explore the impact of the size of electrodes and local charge disorder. The results are relevant for designing the nanoparticle devices with improved conduction; they also highlight the significance of topological descriptions for a broader understanding of the nature of fluctuations at the nanoscale.