Ultrasonic testing techniques such as guided wave-based structural health monitoring aim to evaluate the integrity of a material with sensors and actuators that operate in situ, i.e. while the material is in use. Since ultrasonic wave propagation is sensitive to environmental conditions such as pre-deformation of the structure, the design and performance evaluation of monitoring systems in this context is a complicated task that requires quantitative data and the associated modeling effort. In our work, we propose a set of numerical tools to solve the problem of mechanical wave propagation in materials subjected to pre-deformation. This type of configuration is usually treated in the domain of acoustoelasticity. A relevant modeling approach is to consider two different problems: a quasi-static nonlinear problem for the large displacement field of the structure and a linearized time-domain wave propagation problem. After carefully reviewing the modeling ingredients to represent the configurations of interest, we propose an original combination of numerical tools that leads to a computationally efficient algorithm. More specifically, we use 3D shell elements for the quasi-static nonlinear problem and the time-domain spectral finite element method to numerically solve the wave propagation problem. Our approach can represent any type of material constitutive law, geometry or mechanical solicitation. We present realistic numerical results on 3D cases related to the monitoring of both isotropic and anisotropic materials, illustrating the genericity and efficiency of our method. We also validate our approach by comparing it to experimental data from the literature.