In a two-port system where a square signal passes through a via we can get a HIGH Q resonance structure which could ruin our S21.
I know that resonance is a standing half-wave pattern, so what what causes S21 to plunge?
what what causes S21 to plunge?
S21 is the ratio of power leaving port 2 relative to the power into port 1 so, if S21 plunges, the (effective) input impedance must also plunge in order to have real power entering port 1. So, in this respect you can't really model the via like a parallel tuned circuit because it wouldn't alter S21 at all (output power ratio to input power would be the same but, power input would be very small.
However, thinking of the via as a parallel tuned circuit is convenient for explaining the loss of power reaching the output port. But, you also have to consider the via as a short length of unmatched transmission line. This creates an input impedance to signal source related to the reflected power at the via and, interfere with the S21 measurement.