InDesign is a high end rented tool to publish on paper via PDF. It was kludged by Adobe for epub. Fixed Layout epub is a bit like PDF, neither is a real ebook.
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As for footnotes, they are actually endnotes (i.e. they are all at the end of the main text). This Calibre shows as a pop-up footnote, in other applications, when you click, it throws you to the end of the book and back.
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Endnotes are best as a paragraph each, explicitly linked to and with a link back. Most ereaders, most of the time and most apps will indeed simply work them as any other linked text in a document and won't popup. Calibre Viewer is handy on a desktop/laptop, but it's using a web browser to simulate an ereader. I use it to check system ToC and links.
Only use InDesign for either print replica for large screens (Fixed layout epub3 or PDF) or for paper (via PDF).
Use MS Word or LO Writer (only edit odt, final extra Save As docx) and Paragraph styles for headings, text, footnotes/endnotes (everything). Don't use the built in "insert footnote/endnote", but insert Anchors/Bookmarks at the required places and link to them. 100% reliable. Import Docx to Calibre and convert to epub. You might need to manually edit CSS on any images, but everything else perfect. I've being doing that for 10+ years.
InDesign is really a corporate Desktop Publishing System for PDF/Paper.
If you were doing a text book with a lot of Maths, you might build it in Sigil.
Copy paste the Indesign content to a real wordprocessor, which is normally the start, then that's imported to InDesign for the publishing (but it's rubbish for re-flowable, i.e. real, ebooks.).
While you can have ebook footnotes as endnotes after everything, on an ebook (as with some paper books) endnotes after each chapter can be better if someone doesn't want to go back and forth while reading, which is awkward on some ereaders.
I learnt nearly 30 years ago that it was a mistake to enter text from scratch into a Publishing program rather than a wordprocessor and then import to the publish system. Never type from scratch into InDesign, Sigil, Calibre or any Publishing program/system.