Basically, on that page there are two alternative methods shown of how you can embed a PDF in a lightbox. First, enable the iFrame option on Settings > Media. Then try one or both of these examples:
1.
<a class="nofancybox fancybox-iframe" href="https://downloads.free-jazz.net/files/2009/05/WoodenGun-EBookSample.pdf#toolbar=0&navpanes=0&nameddest=self&page=1&view=FitW,0&zoom=100,0,0">Open in iFrame with class fancybox-iframe</a>
2.
<a class="nofancybox fancybox-iframe" href="https://docs.google.com/viewer?url=http%3A%2F%2Fwww.adobe.com%2Fdevnet%2Facrobat%2Fpdfs%2Fpdf_open_parameters.pdf&embedded=true">Open in iFrame with Google Docs Viewer</a>
Maybe that will work better on iPad?