Good question, you should ask this in the java2d forum because then Dmitri T might answer it, he's the expert engineer from Sun who kindly helps us out.
You're correct that you need openGL on linux and friends and d3d on windows to achieve acceleration.
The problem with webstart is that the display of the download dialogs cause one of the java2d pipelines to be used (the one specified in your jnlp file, or whatever the default pipeline is), which means that you can't switch pipelines yourself programatically since the display was already initialised. If you use an installer or something intead, you can programatically select the d3d pipeline by putting this code in your main class:
The capital T will mean that "Direct3D pipeline enabled on screen 0" will be printed if successful.