A generalized scientific review with elements of additions and clarifications has been carried out on the methods of theoretical research on the electrophysical properties of crystals with ionic–molecular chemical bonds (CIMBs). The main theoretical tools adopted are the methods of quasi-classical kinetic theory as applied to ionic subsystems relaxing in layered dielectrics (natural silicates, crystal hydrates, various types of ceramics, and perovskites) in an electric field. A universal (applicable for any CIMBs class crystals) nonlinear quasi-classical kinetic equation of theoretical and practical importance has been constructed. This equation describes, in complex with the Poisson equation, the mechanism of ion-relaxation polarization and conductivity in a wide range of polarizing field parameters (0.1–1000 MV/m) and temperatures (1–1550 K). The physical model is based on a system of non-interacting ions (due to the low concentration in the crystal) moving in a one-dimensional, spatially periodic crystalline potential field, perturbed by an external electric field. The energy spectrum of ions is assumed to be continuous. Elements of quantum mechanical theory in a quasi-classical model are used to mathematically describe the influence of tunnel transitions of hydrogen ions (protons) during the interaction of proton and anion subsystems in hydrogen-bonded crystals (HBC) on the polarization of the dielectric in the region of nitrogen (50–100 K) and helium (1–10 K) temperatures. The mathematical model is based on the solution of a system of nonlinear Fokker-Planck and Poisson equations, solved by perturbation theory methods (via expanding solutions into infinite power series in a small dimensionless parameter). Theoretical frequency and temperature spectra of the dielectric loss tangent were constructed and analyzed, the molecular parameters of relaxers were calculated, and the physical nature of the maxima of the experimental temperature spectra of dielectric losses for a number of HBC crystals was discovered. The low-temperature maximum, which is caused by the quantum tunneling of protons and is absent in the experimental spectra, was theoretically calculated and investigated. The most effective areas of scientific and technical application of the theoretical results obtained were identified. The application of the equations and recurrent formulas of the constructed model to the study of nonlinear optical effects in elements of laser technologies and nonlinear radio wave effects in elements of microwave signal control systems is of the greatest interest.