I have a one-page InDesign document with 50+ layers. Each layer contains a single logo file, and I need to export the document to a PDF with one layer turned on per page. Ideally, I'd like to export to individual PDF documents, but it would be okay to export to a multi-page PDF as well, and break the PDF into single pages later if needed.
I have recently started using the InDesign Page Exporter Utility Script and i can confirm this does what you need. It gives you the option to export each layer as a separate PDF via a simple interface.