I think I can see where fluid definitions of "page numbers" can cause confusion here.

InDesign has the capability to generate "page numbers" automatically by placing them with special markers (Type>Insert Special Character>Markers>Current Page Number menu command). These are generally used on master pages so they'll automatically be transferred with the correct page number for any document page that's related to that master page, though you can place them on document pages if you have a specific need. If you use this special function of InDesign, no, you won't have to delete the page numbers. Master page items don't export to epubs.

But if you manually put those page numbers on your document pages (using your Text tool to place text with 1, 2, 3, and so on for each page), then you'll need to manually remove them before creating your reflowing epub.

And in either case, if you're creating a fixed epub, like Bob explained, you want to keep them where they are, and by extension, where they belong.

Now for what Derek offered about the challenges of repurposing print books to epubs. Yes, it can be done. But not without some difficulty. It's easier to start from scratch and create a dedicated epub document, which will make things a lot easier on you in the long run. It'll make things a lot easier for you in the long run. You can repurpose the print version, but it's a lot more effort than it's generally worth.

For example, where would you like the Table of Contents? When you normally create a print version of the book, the ToC and Index are usually the last two things you do before sending the job out the door. And you usally place the Index in the back and the ToC before the first page of the manuscript — with pages like the publisher's page and any dedication/foreward pages, in what's generally known as "Front of Book." But if you're assembling your book by reading order, in the order text threads are generated, it'll be right after the Index at the absolute back of book.

This is why many epub designers create a dedicated, streamlined InDesign document for generating an epub. Near universally, you'll find if you're creating a reflowable epub, it's much faster and much easier to tailor a new document from scratch.

The link below is a slightly dated document, but the content's still quite valid and very relevant to your coming task. I recommend it highly:

Ebooks from InDesign: Twenty Things to Consider

Hope this helps,

Randy