Please let your partner know that Amazon also supports 2FA, which would have likely prevented her account from being compromised.
Token based 2FA is another story though... it definitely adds another layer of security to your passwords and amazon supports this format.
In the case of the OP's partner, my guess is that either they were phished into revealing their Amazon password or their password for Amazon was the same password used elsewhere and that source was hacked.
2FA is a general term. U2F is a type of 2FA. The other type, which is what I was referring to, is TOTP (Time-based one time password).
You are right that U2F is more secure. The primary security advantage is that there is no longer a shared secret that needs to be stored on each end. But saying 2FA is useless would be like also saying that U2F is useless since 2FA is a general term.
That said, in this case, TOTP would have likely prevented anyone from accessing the OP's partners account. Therefore, TOTP is not useless per your original comment.
https://m.youtube.com/watch?v=kGGMgEfSzMw&time_continue=1271