WSJT uses portaudio directly and that can talk to jack through its portaudio host if jack has been compiled with that support in it.
Ideally, yes. However, unless some of the WSJT code has been rewritten, despite appearances, you're limited to using the WSJT default sample rate. Sample rate choices made in the audio subsystem aren't actually propagated correctly through the entire DSP chain.
This causes problems with JACK in a number of situations, depending on which driver (ALSA, FFADO, etc.) JACK itself is using.