Mathematical models of multi-layer orthotropic shells were reconsidered based on the Timoshenko hypothesis. A new mathematical model with ε-regularisation was proposed, and the theorem regarding the existence of a generalised solution to the model was formulated and proved. The algorithms of numerical investigation of models studied with the aid of the variational-difference method were developed. The associated stability problem was also addressed. A comparison of the results yielded by the considered models was carried out and discussed for numerous factors and parameters.