Mostly when there is a "rain" effect in them, or the dust in tombs
I think you're talking about the "light rays coming through the roof" type of effect, and the fog that covers the floor in most dungeons and caves.
In certain areas it is very concentrated and causes a significant dip in framerate, as well as input lag.
On your system it may not be evident that the framerate and input lag are connected because the FPS hit isn't too bad. I played Skyrim over the weekend on a 2009 MacbookPro with a Nvidia 9400M! Was pretty stunned that the game would run at all. Had a program to monitor the GPU temp, fan speed, and also overclocked the GPU. Then I created a custom 1152x720 resolution with the Nvidia control panel. This let me play at an average 22-25 FPS outdoors which is pretty nuts all things considered! What was more amazing to me, is just how incredible the load times are, as they were just as fast on that system, with hgih detail textures, that they are on my Core i5/4850 iMac! So I don't think Elder Scroll's engine is as bad as people make it to be... but I digress.
Back to the topic: in caves and dungeons, it would sometimes dip to 5 FPS!
I'm pretty sure it is not related to GPU shadows. This is one of the first tweaks I tried on the Nvidia 9400M, and it made very little difference. You can sort of disable shadows by changing the shadow distance settings in the SkyrimPrefs file:
This effectively removes shadows. I played several hours like this, only to find out later that the GPU shadows had a very little impact on performance. On that system I gained only 1-2 FPS. However the change in graphics quality was huge, because editing the settings as above, turns off a lot of lighting that creats dramatic ambiance. Perhaps there is a better way to turn off shadows, but effectively the settings above turned off more than shadows.
Then, on the SkyrimNexus website you can find the mod Fog Mesh Remover which, as is explained on the description page, does not actually improve performance. Still I tried it thinking that perhaps the GPU would skip the polygon entirely if it is all 0 alpha but it doesn't.
Last but not least there was another setting I saw that was suggested. You can reduce the number of particles like so:
Reportedly, the particles are used to make the "ambiant dust". Having tried this, I found no change in performance. I suspect that the person confused the "dust in the light" texture effect for particles. They are a texture however, which slowly pans to give the impression of dust floating in the air.
Short answer: the fog/light ray/ambiant dust effect appear to be mesh-based, and appears to be fixed in the scenery itself. So there is no setting to turn it off entirely that I know of. Perhaps this will be possible once the Creation Kit comes out starting in January.