Do you mean the URLs inside the document are not clickable?
GDE will translate these into clickable links only if they are clickable in the source PDF. You would have to make the URLs into links in whatever the source document, and save your PDF. Then when you embed that PDF the links will remain clickable inside GDE. (It won’t add links that aren’t already clickable in the PDF itself.)
This is a theory, but it looks to me like the links aren’t actually embedded in the document. I opened the file up in Adobe Viewer XI and the links are indeed clickable, but I think the viewer is adding the link. When I view the source of the PDF, no clickable link regions seem to be defined in the file itself.
The PDF is also in a rather old format (PDF 1.3 – PDF 1.7 has been out for the last 4 years or so) – not sure if this contributes.
If you still have the source document it would be worth confirming that the links are indeed present, and perhaps save it to a newer PDF format. If you don’t, you could also perhaps check this from Adobe Acrobat (if you have it). I have it at work, but not here…