Fixed layout epub will help you achieve the kind of production you want.
Whatever you design in InDesign layout it is matched exactly as it is in the exported fixed layout epub. This exported epub can then be seen in ibooks, on ipad, though there might be some issue with other readers.
To achieve this fixed epub, you just have to layout your document in InDesign and export it to the format epub(fixed).
To your concern about hyperlinks, yes this is not yet supported.
I've moved your question to the InDesign EPUB forum, the best location to talk about fixed layout ebooks.
The main thing about fixed-layout epubs is that they work in very few places. You could try opening it in the Readium plugin in Chrome, in iBooks desktop, or on an iPad (iBooks, Kobo iOS app, etc.) If you aren't on a Mac, I don't know how else you could open it on your desktop.