Given they already support standard WebAuthn (passkey or other), I think it’s a pretty safe guess to say they’ll support Yubikeys. I can’t find any written confirmation yet though.
I don’t think this is directly related to the E2EE announcement, rather it is an option to replace the current MFA method of receiving codes on your Apple devices.
> [Apple] will now allow users to log in to their Apple accounts with hardware-based security keys made by other companies such as Yubico.