Also, blocking base64 encoding would block email schemes where digital
signatures are used.
That is entirely mistaken. You might want to ensure that sender and
recipient agree on whether to sign the encoded or plaintext versions
of the message, but that's all.
I wouldn't propose BANNING base64 encoding... not at all. But I don't think
there's much if any point in including it in E-mails if the recipient isn't
ready to accept it. If a recipient is prepared to accept base64 encoding from
specific senders (those for which they have a public key, for instance) then
it's easy enough to turn base64 permission on for those trusted senders.