At some point (2020) Thunderbird stopped using Enigmail. Native support for GPG doesn’t (easily) allow you to use sub-keys stored on a Yubikey for signing or encryption. It is possible to tell Thunderbird to use one external key but this doesn’t work if you have separate sub-keys for both message signing and encryption.
This guide shows how to create and export a temporary key containing both the signing and encryption keys for use in Thunderbird.