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In the Export Adobe PDF window, choosing a different compatibility (the drop-down in the upper right) makes the Bookmarks, Hyperlinks, and Visible Guides and Baseline Grids in the Include area become available. Choosing different standards affects it as well, usually making them unavailable. I haven't spent much time experimenting with it to see how it affects output.
[Branched from March 2013 discussion about InDesign CS5.]
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I believe what you are seeing is normal behaviour. As long as you have a PDF/X standard selected, hyperlinks/bookmarks will be greyed out. Change the PDF/X standard to 'None' and you'll see things change back.
This is because
To retain maximum interactive features in a PDF you create:
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Make your PDF for professional print OR for interactive use. If you need both purposes, make two PDFs.