Not sure exactly what your issue is. Do you have an example of a file that is NOT working?
Your example <a> tag works just fine as long as you are only linking to IDs in the same html document. Even though it is not required to split the html document - it is much more common than not. Ebook rendering is much more efficient with smaller file sizes. Most people will split on every chapter or when they want to ensure an item is on its own page.
If you want to link to a different page you need to use the full reference in your tag eg. <a href="Chapter01#footnote1">Yo</a>.
If you are using a specialized ePub software like Sigil or Calibre, then it will automatically fix the links when the HTML page is split -
as long as they are valid links to begin with.
Cheers,
PS. Sigil and Calibre will also automagically create a TOC for you. You can then edit them manually....makes life very easy!