As far as I know, even older versions of Java3D use JOGL under OS X, Java3D 1.6.0 and later aren't in a worse position than older obsolete versions.
Apple won't drop OpenGL support, simply because tons of softwares use OpenGL. If it did so, it would lose a lot of customers. Lots of companies don't want to maintain a completely separate code path for OS X, especially for non gaming softwares (CAD for example).
Java3D isn't a good choice for the future as no new features will be implemented (except a few things brought by some contributors). There won't be any new renderers relying on Metal and Vulkan in Java3D.
If there was no support of OpenGL, yes it would really matter for Java3D and JOGL softwares as JOGL is a Java binding for the OpenGL API, it's not magic: no OpenGL => no JOGL => no Java3D.