When the client bits are enabled, we should depen on media-libs/libsdl[opengl] instead of media-libs/libsdl[joystick]. I had no issue to run quake3 with joystick disabled but I wasn't able to run quake3 without opengl (sdl complains because it can't open libGL.so.1).
You don't need to enable the joystick but libsdl does need to be built with USE=joystick. Added the opengl use flag as well. thanks for the bug report.