CAD used to be digital abstraction of the physical media that is 2D drawings on paper, so XY is the plane of the paper going horizontal/vertical, and most detailing are in vertical cross sections so Y ended up being up most of the time.
The Z axis is then Frankensteined into the existing system to get a proper 3D representation, so it became the depth axis for the existing XY plane.
In Minecraft it’s even more evident as Notch Frankensteined the Z axis into a game engine that’s originally developed for side scrolling.