This has most probably nothing to do with Freemarker. What you are observing is an issue depending on how e-mail clients handle and display e-mails. Some clients just try to "help", identifying web and e-mail addresses etc. and then making them links.
Depending on the Mime type, different mail clients have different ways handling/displaying e-mails. Outlook e.g. sometimes does not display all attachments. It is anything but trivial to send out e-mails that display well in every mail client out there.
This thread on sevenforums.com states that you can trigger hyperlink replacement on or off in the options:
- File > Options > Mail > Editor Options > AutoCorrect Options > AutoFormat tab > Replace > Internet and network paths with hyperlinks