Official comment
So, I asked the product team to shed a bit more light on this for me as I haven't had much hands-on experience with the DJM-900NXS2 and rekordbox...
With the DJM-900NXS2, either FX1 or FX2 can be used alternately because NXS2 has a Send/Return feature to enable post fader FX, and in this situation, only one FX can be selected.
FX2 is not disabled; both FX1 and FX2 will be applied to the channel selected by FX1 on the left side of the screen. FX1 -> FX2 is connected in tandem, you simply can't assign them separately.