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What I suggest above works on a Kobo and most other ereaders.
Links inside an ebook use anchors, they are easily created in a wordprocessor at the start of any heading or paragraph. The anchor is named by you such as f22 for footnote 22 or ch11 for "Chapter 11: Five Have a Picnic". Then the URL in the link is #f22 or #ch11
You are best to build a table of contents this way and then the ebook creation (such as Calibre) uses it to build the system TOC / NCX.
There is a way to do popup windows, but support is poor. I'd use it if it was universal. Kobo eBooks is less than 10%. The regular epub works the same on a Kobo as any other ereader that uses epubs. The kepubs is mostly extended rendering and is ONLY on Kobo.
Use any wordprocessor with styles for paragraphs and headings. The use of Anchors (bookmarks) and Links is the same in all.
If a footnote is less than two lines just use a paragraph style that is right justified, slightly smaller alternate font and put the text inline as a new paragraph with [ around it]
Regular footnotes are distracting to the flow of reading. It's worse in ebooks even if the popup kind. There is no concept of a fixed page. Page boundaries change according to font, margin, resolution, screen size.
Save Docx, use Calibre to create the ebook. Or if it's complex (links are not), use Sigil.
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