Phononic properties are commonly studied by calculating force constants using the density functional theory (DFT) simulations. Although DFT simulations offer accurate estimations of phonon dispersion relations or thermal properties, but for low-symmetry and nanoporous structures the computational cost quickly becomes very demanding. Moreover, the computational setups may yield nonphysical imaginary frequencies in the phonon dispersion curves, impeding the assessment of phononic properties and the dynamical stability of the considered system. Here, we compute phonon dispersion relations and examine the dynamical stability of a large ensemble of novel materials and compositions. We propose a fast and convenient alternative to DFT simulations which derived from machine-learning interatomic potentials passively trained over computationally efficient ab-initio molecular dynamics trajectories. Our results for diverse two-dimensional (2D) nanomaterials confirm that the proposed computational strategy can reproduce fundamental thermal properties in close agreement with those obtained via the DFT approach. The presented method offers a stable, efficient, and convenient solution for the examination of dynamical stability and exploring the phononic properties of low-symmetry and porous 2D materials.