I'm pretty sure LWJGL uses jinput behind the scenes for input handling (at least it used to), so you will likely get the same behavior with both libraries.
I wrote an application a while back that used some
really hacky code to re-initialize Jinput to rescan for joysticks, which might be somewhat helpful. IIRC, the controller listener hooks worked correctly on Windows, but that hack was necessary on Linux.
It's been a while, so I forget how I dealt with the native libraries, but that application might also be able to help with that.