Kurt Revis describes reading hypertext as a three stage process. He also wryly notes that hypertext is the perfect medium for expressing confusion.
One solution to this problem is to allow the user to see the links on request. The text is usually uninterrupted, but can be changed to display where links are to be found. Of course, the user now has to stop reading in order to display the links, so this solution may not be so satisfactory after all.