The work is a continuation of research devoted to substantiating the reliability of solutions obtained by the finite element method for the analysis of nonlinear deformation, buckling and vibrations of thin elastic shells under the action of thermomechanical loads. The method is based on geometrically nonlinear relations of the three-dimensional theory of thermoelasticity and the principles of the moment finite element scheme. A thin elastic shell of an inhomogeneous structure is modeled by a universal spatial isoparametric finite element. The modal analysis of the shell is implemented at each step of the static thermomechanical load. The subspace iteration method is used to determine the spectrum of the lowest frequencies of natural vibrations of shells. A shallow spherical panel with a square plan is considered. The effect of preheating on the loss of stability and vibrations of an elastic isotropic shell under uniform pressure loading is investigated. The behavior of the shell weakened by two pairs of cross-channels is analyzed. The weakening of the panel by narrow and wide channels, which can be eccentrically located relative to the middle surface of the shell, is considered. The effectiveness and adequacy of the method is confirmed by a comparative analysis of solutions with results obtained using modern multifunctional software systems LIRA-SAPR and SCAD. The features of using the systems for solving the problems under consideration are given. Analysis of the results made it possible to evaluate the possibilities of using these software systems to substantiate the reliability of solutions to certain classes of problems of geometrically nonlinear deformation, buckling and vibrations of elastic shells.