Yes, the energy is conserved.
Work Step by Step
The vibrating particles in the medium have both kinetic and potential energy (e.g., if a rope is displaced from equilibrium, there is elastic potential energy stored in it). Even when two waves interfere destructively and it seems like energy has disappeared because the instantaneous displacement of the medium is zero, the individual particles of the medium are moving and possess KE. In the absence of dissipative forces, energy is conserved.