when solving for waveport, hfss solves the 2D eigen value problem to find the propagating modes in the waveguide, their characteristic impedance and their propagation constants. It does not actually solve the structure, so you won't be able to find S11 or the radiation pattern for example.
This is usually used to make sure that the mode that hfss will use is actually the mode you want to excite and to check your port setup.