Well there is also the benefit of not needing to distribute a native DLL, so it will work anywhere that Java runs, without security restrictions. Like unsigned applets and Web Started applications.
It will be easier for anyone to build for the same reason.
The only way I see the performance NOT getting a boost, is if the ODE native code uses SIMD instructions to optimize some things. I don’t think there are still a lot of issues with Java’s floating point that would restrict the performance enough that getting rid of the JNI call overhead wouldn’t balance out.
Either way, I think there are enough reasons to have a pure Java version of ODE that even if there was no performance gain at all, it would still be better. Though I guess without operator overloading it will look a bit messier on the insides.