Os cabeçalhos das mensagens (dos quais o assunto é um deles) não podem ser criptografados.
Se o assunto for sensível, deixe em branco.
This is an ever coming back request and my answer is always the same: Enigmail implements/supports the standards available for encrypting&signing emails. These are defined in RFC 4880 (OpenPGP) and RFC 3156 (PGP/MIME). I will not implement any Enigmail-specific solution that is not defined in a standard, and therefore the subject is currently not encrypt-able.