Hi Jonathan,
Here is the official open bug report for epubcheck 3 which is targeted to be closed in epubcheck 4.
https://github.com/IDPF/epubcheck/issues/305
There are times the doctype is needed for the ncx to actually work. That is why pre-release versions of epubcheck4 now allow the doctype on the toc.ncx.
Take carw,
KevinH