With OpenGL, there wouldn't be any significant difference when running FS-UAE in X or on the framebuffer.
But if you are running FS-UAE through a compositor on X, that can indeed impact the performance and smoothness of the display, so either disabling compositing when running FS-UAE, or running FS-UAE in fullscreen (provided that the window manager unredirects FS-UAE when in full-screen) is a good idea.
