I've had to look this up twice now, so time to post it here.
Thunderbird will use Firefox to open email links, even if Chrome is your default. The solution is to go into Preferences->Attachments and change the browser used for links, however this option may or may not be present. If not, you have to go into ~/.thunderbird/<whatever profile name>/ and replace the mimeTypes.rdf with the one from the link above.
After this start firefox, and the options should now exist in Preferences->Attachments.
Another option if this fails to work comes from https://community.linuxmint.com/tutorial/view/1391 whereby the config editor is used to make Thunderbird ask your preference for links by setting the following strings to true:
ReplyDeletenetwork.protocol-handler.warn-external.http
network.protocol-handler.warn-external.https
network.protocol-handler.warn-external.ftp