A toc.ncx is required for EPUB2.
A NAV document is required for EPUB3.
Sigil's ToC tools always operate on the required element--according to the current EPUB's version--and neither can be deleted. The exception is the completely optional "Create HTML Table of Contents" tool (which does the same thing regardless of the EPUB's version--build an optional html toc from the required internal toc.)
A NAV document may look like a regular old html file to the uninitiated, but it's not.
Sigil includes an empty NCX in all EPUB3s. It's your choice if you want to bother manually keeping the NCX in sync with the required NAV for backward compatibility with EPUB2 reading systems. The only way to remove the NCX from an EPUB3 is to use a Sigil
Output Plugin to save a copy of the EPUB after all editing is done. You just have to remember that if you ever need to use Sigil to edit that EPUB again, you'll need to use the NCXRemove output plugin again.
I've no idea where your "2 extra toc"s might be coming from, or what they might represent. Not enough info.