Most everyone is using a front end that hides the command window so that you never see that. Only way I know to get rid of it would be to comment out the following line of code in video.c of the mame source files and recompile:
mame_printf_info("Average speed: %.2f%% (%d seconds)\n", 100 * final_emu_time / final_real_time, add_subseconds_to_mame_time(global.overall_emutime, MAX_SUBSECONDS / 2).seconds);