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You can have headers and footers at a document/file level in html5 but it is not easy to get running page headers and footers since page size is variable and unknown. In epub3 you can simulate it using an aside tag, some css such as "display: oeb-page-header" and/or javascript to open a pop-up window. I am sure there are other ways to simulate it as well.
But only the reading device know its page size and only it can allocate space in its window layout for each page of text for something like a running header or footer. It is typically not part of the epub itself, but of the device. Same with pop-up footnotes.
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