The file iTunesMetadata.plist may be in the EPUB - but I don't think Sigil will display it. It doesn't 'see' it since it's not supposed to be there.
You can look for it by unzipping the epub (an epub is just a zip file) using your unzip or unarchiving software. You may need to rename it to file.zip to be able to unzip it.
You can then remove the file and zip it back up. This is what the modify epub plugin can do.
I would be interested to know if anyone using the 0.6.902 beta can test out an epub with the .plist file to confirm. In a brief test of creating an epub with a fake iTunesMetadata.plist in the top level directory, when I open it, the file is not visible in the folders. And after I save the epub, and later unzip it, the .plist file is gone. I don't know if 0.6.2 behaved the same way.