I think that perhaps the toc.ncx is a mandatory item in an ePub, and therefore calibre generates a default when you do not create one.
I checked a small ePub with the IDPF validator, (
http://validator.idpf.org/), after removing the toc.ncx file and its reference in content.opf: it failed validation with a message that indicated the ncx was missing. Putting the toc back caused it to pass validation, comfirming that this file is required.