To quote the guy from Wag The Dog, "This is nothing!"
Seriously, they're not an issue. The Linux kernel will complain because the Nvidia drivers contain some closed-source portions, thereby "tainting" the license of GPL'd kernel. And Mesa (the OpenGL replacement for Linux) comes with non-accelerated versions of the libraries you mentioned (libGL, libglx, etc.). The ones that come with Mesa are renamed in case you ever unload the drivers. You should be good to go.