Having the xml declaration/header is not required by all systems I think. That said the DOCTYPE is important for setting the allowed xhtml entity definitions, if it should be interpreted as strict or transitional rulesets, and quirks and things. Having it missing in a xhtml file is not the best idea especially when the pages are served up as xhtml/xml vs html.
I am surprised that epubcheck did not flag it with at least a warning if not an error.
Running Sigil's Mend will fix any missing xml header and fix any missing doctype automatically based on the epub version.
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