The solar atmosphere is a complex, coupled, highly dynamic plasma environment, which shows rich structuring due to the presence of gravitational and magnetic fields. Several features of the Sun’s atmosphere can serve as guiding media for magnetohydrodynamic (MHD) waves. At the same time, these waveguides may contain flows of various magnitudes, which can then destabilise the waveguides themselves. MHD waves were found to be ubiquitously present in the solar atmosphere, thanks to the continuous improvement in the spatial, temporal, and spectral resolution of both space-born and ground-based observatories. These detections, coupled with recent theoretical advancements, have been used to obtain diagnostic information about the solar plasma and the magnetic fields that permeate it, by applying the powerful concept of solar magneto-seismology (SMS). The inclusion of asymmetric shear flows in the MHD waveguide models used may considerably affect the seismological results obtained. Further, they also influence the threshold for the onset of the Kelvin–Helmholtz instability, which, at high enough relative flow speeds, can lead to energy dissipation and contribute to the heating of the solar atmosphere—one of the long-standing and most intensely studied questions in solar physics.