the standard behavior across all apps that send Growl notifications
(on Windows, at least) is that left-click triggers their action, if
any, and right-click closes the notification. so if you see a
notification you want to act on, click it. otherwise, you have a few
options:
1. right-click instead to dismiss (as you mentioned)
2. do nothing and let the notification timeout on its own
3. Alt-X keyboard shortcut to dismiss the notification
if a notification has no action associated with it, then left-clicking
will essentially do the same thing as right-clicking. behind the
scenes, it is different though. you left click, it fires action (none,
in this case) and closes the notification.
if the Thunderbird plugin and/or Thunderbird is not opening the
correct email when left-clicked, then that is a bug. i will take a
look to see if i can fix it.