Currently Thunderbird has its own password manager, but it offers two possibilities: either you don't encrypt the password stored, or you use another password to encrypt the actual one for e-mail. This sounds quite useless to me, so I would prefer to store Thunderbird passwords in GNOME keyring. Hope this is possible.
There is an extension called GNOME Keyring integration.
Have not yet tried it but: https://github.com/infinity0/mozilla-gnome-keyring#readme