We look for manifestations of quantum interference effects in the Seebeck coefficient of a molecular junction, when the electronic conductance exhibits pronounced destructive interference features due to the presence of quasi-degenerate electronic states which differ in their spatial symmetry. We perform our analysis by considering three separate limits for electron transport: coherent, fully dephased, and suffering inelastic scattering with molecular vibrations. We find that while the conductance displays strong signatures of the underling transport mechanisms: destructive quantum interference features in the coherent case and thermal activation characteristics in the inelastic limit, the Seebeck coefficient conceals details of electron dynamics while it robustly reveals information about the energy characteristics of the junction. We provide closed-form expressions for the electronic conductance and the thermopower of our system as a function of temperature, gate voltage and hybridization energy in different transport limits, then exemplify our analysis on a specific conjugated molecule with quasi-degenerate orbitals of different spatial symmetry.