The .xlsx file is actually just a compression archive (zip file) so if you truly want to add a hidden file then you could just add a .xml file to the archive. That way Excel wouldn't even know it was there.
Rename a .xlsx file to .zip, extract it, add your file, then select the contents of the .zip file and re-archive them. Rename to .xlsx and you'll have your hidden .xml file inside there.
(NOTE: Do not zip the top-level folder, only the contents)
You can do this in C# using a zip library like SharpZipLib:
http://www.sharpdevelop.net/OpenSource/SharpZipLib/
UPDATE: This "hidden" file will not be preserved if the user saves the file from within Excel. The best idea I can come up with for that scenario is to invoke the code as part of a VBA macro embedded in the sheet.
This link contains useful information about manipulating the parts of an Office package: http://msdn.microsoft.com/en-us/library/aa982683.aspx
The core.xml and app.xml (in the docProps folder) contain the document properties and might be a good location to store additional xml information.
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