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1: As you know, S is amplitude parameter. So abs^2 is the intensity/power parameter. For 2X2 device, abs(S11)^2 is power reflection and abs(S21)^2 is the power transmission for the specific mode.
2: if you want to get result in dB, for abs^2, it is 10log10. for abs(S), it is 20log10.
BTW: you mentioned you sweept wavelengh in FDTD? in the port/mode case, once you use broadband, you do not need to sweep since FDTD can give you broadband result from one simulation.
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