Let's try this:
In thunderbird go to Edit->Preferences->Advanced->General->Config Editor
search for these preferences:
network.protocol-handler.warn-external.http
network.protocol-handler.warn-external.https
network.protocol-handler.warn-external.ftp
And set them to true by double-clicking on them
Now when you click on a link it should ask you what to use for it to be 
opened(just for the first time, it should remember your pick afterwards).
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https://bugs.launchpad.net/bugs/880834

Title:
  URLs in message body not opening in browser

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