The localized magnon modes of isolated $k\pi$ skyrmions on a field-polarized background are analyzed based on the Landau-Lifshitz-Gilbert equation within the terms of an atomistic classical spin model, with system parameters based on the Pd/Fe biatomic layer on Ir(111). For increasing skyrmion order $k$ a higher number of excitation modes are found, including modes with nodes in the radial eigenfunctions. It is shown that at low fields $2\pi$ and $3\pi$ skyrmions are destroyed via a burst instability connected to a breathing mode, while $1\pi$ skyrmions undergo an elliptic instability. At high fields all $k\pi$ skyrmions collapse due to the instability of a breathing mode. The effective damping parameters of the spin waves are calculated in the low Gilbert damping limit, and they are found to diverge in the case of the lowest-lying modes at the burst and collapse instabilities, but not at the elliptic instability. It is shown that the breathing modes of $k\pi$ skyrmions may become overdamped at higher Gilbert damping values.