Java 3D 1.5.2 internally benefited of hardware acceleration thanks to 3 backends including 2 native ones (Direct3D, OpenGL) and the last one based on JOGL 1. Java 3D 1.6 uses a single backend based on JOGL 2 but it is transparent for the developers, you have nothing to change in existing examples relying on Java 3D. You can still use Canvas3D. Keep in mind that Java 3D alone is unable to communicate with the graphics card, that's the role of JOGL. You don't need to use JOGL canvas (NEWT GLWindow, AWT & SWT GLCanvases, Swing GLJPanel, ...), you can use Java 3D canvases
and benefit of the hardware acceleration through JOGL 2.
Mixing pure JOGL rendering with Java 3D may require the use of a JOGL canvas.
The main interest of porting Java 3D to JOGL 2 is the benefits of its bug fixes. The maintenance of JOGL 1 has been stopped several years ago and as the previous version of Java3D is based on it, it doesn't benefit of these bug fixes. For example, the previous version of Java 3D doesn't work on recent Macs.
Edit.: The webmaster of
http://www.interactivemesh.org comes here sometimes, maybe he can help you if you really want to mix JOGL and Java 3D.