With mods and shaders and everything I got an average of 50-60 FPS (measured with MGE's FPS Counter) in a certain indoor location. Once I had toggled my menus off, this was up to 80. I have tested this over and over to make sure it's not a coincidence related to NPCs moving around or something, but I'm absolutely sure now.
I did notice that when I had the default Morrowind FPS counter active it would not increase FPS when I turned the menus off. But it's not a glitch with MGE's FPS counter, the increase in FPS with menus off is real: it really does play a lot smoother. So I guess that whatever is causing the FPS 'loss' with the menus on is also causing the loss with the default MW FPS Counter active.
It also seems that there isn't much of an improvement if my FPS is already very low. When I went to an exterior cell where I had 15 FPS average there was barely any difference when I toggled menus off, but in a place inside where I got 50 it changed to 80. In a different outdoor place where I got 30 it changed to 40-45.
Even without any mods, MGE, MCP or the FPS Optimizer: It still happens.
Any idea what could possibly cause this? It would be great if I could somehow have the same FPS of having the menus off when the menus are on. Does this happen to anyone else? Could someone else test it (Not with the default Morrowind FPS counter.)?