Two reason:

• Frequently having multiple words as hyperlinks in ebooks mean that 'turning the page' may instead change chapters. Maybe it is just a problem with iPhone kindle.
• For links that reference forward chapters, what is a new reader to do? They can ignore it and not understand the reference, or they can click, read, and then try to go back... but it's not a very smooth reading experience.

Granted, I probably wouldn't have noticed the second issue, if not for the first issue.