Hello,
It think the problem you are having is not really a problem, just a difference in the presentation of the emails to you. If you compose an email in Thunderbird and put a link in it the link will still be clickable on the receiving end. Try it out! Send an email using Thunderbird to a free account such as a Gmail account and you will be able to click the link. I leave my preferences set to send plain text email messages and have no problem sending links.
-Raymond