I'm currently developing an IE add-on that needs to read some existing files under the "My Documents" from the current user's profile.
If IE is running in protected mode:
Thank you very much.
Have a look at Understanding and Working in Protected Mode. When running in Protected Mode, IE is running as a low integrity process. Low integrity processes can only write to low integrity write locations. I think you should be able to read from My Documents, as long as the user has normal permissions to read from there.
Just go ahead and write the code and try it. If you encounter specific problems I would come back and ask those as a separate question.