Under Linux (Ubuntu and its derivatives for sure) there is only one way to amend this. Go to .mozilla-thunderbird, find the directory for your profile (something like rv7dwavi.default) and open the file prefs.js.

Then search for the strings  network.protocol-handler.app.http and network.protocol-handler.app.https.

Usually these directives are missing so you can safely add them anew as follows:

user_pref("network.protocol-handler.app.http", "google-chrome");

user_pref("network.protocol-handler.app.https", "google-chrome");

That's all and from now on Thunderbird will open all links in Google Chrome.