The MAME FPS does include any slowdown caused by GLSL
Are you sure about this?, maybe I'm doing it wrong, but running: "mame pacman -nothrottle -str 300" with and without GLSL gives the exact same "Average speed" output.
However, the "-sdlvideofps" did the trick and told me that I was actually rendering at ~24 fps. I was hoping this card could handle GLSL at this resolution, will keep trying options and resolutions now that I have a way to measure.