Probably because OpenGL is not 100% available on all the platforms that Java is available for.
So, for example, Java3D has bindings to both DX and OpenGL to provide a layer of abstraction.
This probably won’t change until/unless OpenGL becomes available everywhere. It’s getting there, but certainly was not as far along when J3D (for example) was designed.
Also, each of the bindings is intended for a different type of usage and different audience. For example, jogl doesn’t support VR caves or VR goggles (does it?) while Java3D does. Jogl is low-level and high-performance, while Java3D is high-level and low(er) performance.
Not everybody is writing games using those tools.
Could it be all redesigned from scratch now that the landscape has changed? Probably. Is it worth it to Sun? Probably not.