Lifetime of non-equilibrium (hot) phonons in biased GaN heterostructures with two-dimensional electron gas channels was estimated from hot-electron fluctuations. Dependence of the lifetime on the electron density is not monotonous -the resonance-type fastest decay serves as a signature of hot phonons. The signature is resolved in nitride heterostructure field effect transistors when the gate voltage is used to change the channel electron density. The transistor cut-off frequency decreases on both sides of the resonance in agreement with the enhanced electron scattering caused by longer hot-phonon lifetimes. The signature is also noted in device reliability experiment: the enhanced temperature of hot phonons, possibly, triggers formation of new defects and accelerates device degradation.