If your bookmarks are tied to the appaerance of text where a distinct paragraph style is applied use InDesign's TOC feature and create a Table of Contents with all the text in that style.
The TOC text frame(s) could be positioned on the pasteboard of the first spread if you like. In the TOC Style you could check the bookmarks option if you export to PDF. That would create bookmarks in the Bookmarks panel for the document.
Regards, Uwe Laubender ( Adobe Community Professional )