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
Unfortunately, looks like it is not possible in the latest Firefox/Thunderbird versions any longer. Refer to https://bugzilla.mozilla.org/show_bug.cgi?id=1321508 for more information.