The ToC in an epub2 is an *.ncx file (often named toc.ncx)
The ToC in an epub3 is an *.xhtml file (often named nav.xhtml). For this reason your epub is certainly an epub3.
The *.ncx is not mandattory in an epub3, it's there only for retrocompatibility purrpose, for old devices, and can be deleted without problem.
The ToC editor of calibre recreates it automatically. As your eReader seems to be using the ncx ToC, it's wise ti recreate it, but maybe it's not even necessary (will your device use the nav.xhtml if there is no toc.ncx?)
For information, you can see the version of your epub in the *.opf file (in the same section than nav.xhtml), in the second line :
<package xmlns="http://www.idpf.org/2007/opf" unique-identifier="BookID" version="3.0">
Also for information (not needed here), the editor of calibre has a tool to convert epub2 to epub3 (in the menu "tools")