I noticed that in Jedi Knight Dark Force II & Mysteries of the Sith the music plays but there are no in-game audio effects if I run the games with A3D-Live installed on the system. In the menu and in the MotS in-game cutscenes the sound effects are working fine, but during playing they are turned off.
Enabling or disabling the specific option doesn't change that behaviour, but uninstalling the A3D-Live wrapper makes the Aureal 3D positional audio options checkbox to dissapear in the audio tab of the settings and makes also the sounds effect to work correctely again.
Since I like the A3D-Live effects, and I use it for Outlaws, which is another LucasArts title that I guess uses the same version of the Aureal 3D, I was wondering if it is supported and if there's a way to make them work on Jedi Knight and Mysteries of the Sith as well.

I've experienced the same. Outlaws sounds a bit better with A3D-Live, but Jedi Knight is muted. My guess is that Outlaws (which used the older, Dark Forces engine) used A3D only for environmental effects, while we know that Jedi Knight used it for true 3D sound. A3D-Live doesn't actually allow for 3D sound. It's just a re-packaging of Aureal's A2D support files for getting 2D sound (+ maybe environmental effects, hence Outlaws sounding differently) on non-Aureal hardware from games designed for A3D (as a way to promote adoption of their API). I guess that Jedi Knight either expects the full implementation of A3D or none at all, so that's why all sounds are muted for us. If so, there might not be any way to fix it, short of someone figuring out how to restore real A3D, but it's been 15 years and no one has.

I can't comment on the previous post, though I have written a guide that covers A3D setup for modern Windows PCs:
https://www.gog.com/forum/star_wars_dark_forces_series/jedi_knight_dark_forces_ii_remastered_2018_guide