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Wall cooling has substantial effects on the development of instabilities and transition processes in hypersonic boundary layers (HBLs). A sequence of linear stability theory, two-dimensional and non-linear three-dimensional DNSs is used to analyze Mach~6 boundary layers, with wall temperatures ranging from near-adiabatic to highly cooled conditions, where the second-mode instability radiates energy. Fluid-thermodynamic analysis shows that this radiation comprises both acoustic as well as vortical waves. 2D simulations show that the conventional "trapped" nature of second-mode instability is ruptured. Although the energy efflux of both acoustic and vortical components increases with wall-cooling, the destabilization effect is much stronger and no significant abatement of pressure perturbations is realized. In the near-adiabatic HBL, the wavepacket remains trapped within the boundary layer and attenuates outside the region of linear instability. However, wavepackets in the cooled-wall HBLs amplify and display nonlinear distortion, and transition more rapidly. The structure of the wavepacket displays different behavior; moderately-cooled walls show bifurcation into a leading turbulent head region and a trailing harmonic region, while highly-cooled wall cases display lower convection speeds and significant wavepacket elongation, with intermittent spurts of turbulence in the wake of the head region. This elongation effect is associated with a weakening of the lateral jet mechanism due to the breakdown of spanwise coherent structures. In moderately cooled-walls, the spatially-localized wall loading is due to coherent structures in the leading turbulent head region. In highly-cooled walls, the elongated near-wall streaks in the wake region of the wavepacket result in more than twice as large levels of skin friction and heat transfer over a sustained period of time.