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I think the answer would depend on how comfortable you are working with the raw HTML code...
If you are OK with it, then Sigil (and I'm pretty sure Calibre) has a 'merge' feature that will remove the separate headers/footers and leave them combined into a single file. That process works well if the css is similar - or you make the css similar before merging.
If you are saying "what's raw html code" then I would suggest leaving the pages separate. You can still bundle them into an ePub - there is no requirement to have everything as a single page. It is actually more preferred to keep the files in ePubs separated logically, such as chapters. Both Sigil and Calibre editor can perform this function admirably. When you read the ePub, with the pages as separate files, it just requires a swipe/tap when transitioning from one file to the next.
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