Where is the indexing designmap file stored?

It's not in a separate file. Indexing information is held in individual .indd files. I'm sure you can find it all by exporting IDML, renaming the file to .zip, extracting, opening up the designmap.xml file, and finding the Index tag in there. 

Honestly, I imagine that you must already know this - otherwise why would you have included the term "designmap" in the title of your post? I am also honestly unsure about exactly how indexing works in books; however, I just made a fake book, marked some references, added some topics, generated an index, saved the book & chapters, then exported IDML, renamed as .zip, and popped open the designmap.xml of those chapters to look. As I expected, each chapter held its own indexing information, and there wasn't anything in the .indb that I could spot. I imagine that, when you check the "Book" box on the Indexing panel, and then you Generate Index, that the indexing tool just walks through all the chapters, gathering the index chapter by chapter, and then combining it all before it gives you a place gun loaded with your freshly generated index. 

So, even though this answer is a little outside my typical area of InDesign expertise, I'm going to speculate that there isn't any place outside the .indd where any indexing info is stored, and that if you're backing up your book, you are also backing up your index. I haven't seen the inside of Subversion in a very long time, so I don't know how that end of your workflow operates.

If you have more questions, I'll happily take a swing at them. Alternately, we can wait for one of the other regulars who knows InDesign's indexing tools better than myself to show up and school us.