Fluid-coupling effects lead to a complex dynamical behavior of immersed spent fuel assembly storage racks. Predicting their responses under strong earthquakes is of prime importance for the safety of nuclear plant facilities. In the near-past we introduced a simplified linearized model for the vibrations of such systems, in which gap-averaged velocity and pressure fields were described analytically in terms of a single space-coordinate for each fluid inter-rack channel. Using such approach it was possible to generate and assemble a complete set of differential-algebraic equations describing the multi-rack fluid coupled system dynamics. Because of the linearization assumptions, we achieved computation of the flow-structure coupled modes, but also time-domain simulations of the system responses. However, nonlinear squeeze-film and dissipative flow effects, connected with very large amplitude responses and/or relatively small water gaps, cannot be properly accounted unless the linearization assumption is relaxed. Such is the aim of the present paper. Here, using a similar approach, we generalize our theoretical model to deal with nonlinear flow effects. Besides that the proposed methodology can be automatically implemented in a symbolic computational environment, it is much less computer-intensive than finite element formulations. Using the proposed technique, computations of basic flow-coupled rack configurations subjected to impulse excitations are presented, in order to highlight the essential features of such systems as well as the relevance of squeeze-film and dissipative effects. Finally, more realistic simulations of complex system responses to strong seismic excitations are presented and discussed.