Well, First off, that mod set is prob outdated. There's a Guide to Editting Textures/ removing armor parts from Naurdon somewhere in the forums.
To fix the Invisible Armor/Body stuff, you need to use the recent game files, meaning extracting old mod textures or such and replacing them on the newer game files
If you want to remove armor, you can, however if you want skin to be there, you can't if there is no mesh/Body underneath it. Overall, what's there is there to be removed or kept unless you want to do heavy modding of the models.