I know you specifically mentioned iBooks, but I was reading the Amazon Kindle publishing guidelines - and while the ePub doesn't need it, Amazon really wants an inline HTML TOC in there...
3.3 Table of Contents Guidelines
Amazon strongly recommends the use of an HTML TOC for all books that would benefit from this navigation feature. This applies to most books, with the exception of fixed-layout children's books (see section 4) and fixed-layout graphic novels/manga/comics (see section 5).
...yada yada...with guidelines on how to do it.
I'm assuming that Amazon enforces their guidelines??
I would check the iBooks guidelines to see if Apple requires anything similar.