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What should be changed is the limitation of only being allowed to send messages in clear. This prevents *any* Internet communication over amateur radio frequencies, as most Internet services are now encrypted. In the remaining amateur radio bands, people should be able to send whatever kind of data they are working on, even ecrypted one, as digital data is per se a form of encryption.
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Quoting from my amateur radio licence here in New Zealand "
Communications must not be encoded for the purpose of obscuring their meaning...".
My take on this is that digital data encoding (RTTY, AX.25, PSK31, ARDOP, etc) is just fine, provided that you are not hiding the meaning of your message (anyone with the right know-how can listen in) - however, using TLS or AES etc to encrypt your message so that only a select few who have the encryption key can decode it is definitely not ok (so no HTTPS over packet radio). If you are developing a brand new digital protocol, merely publishing a protocol description on your web site and or writing a descriptive article to a ham radio magazine (NZART Break-In, ARRL QST, RSGB Radcomm, etc) is probably sufficient to satisfy "not encoded for the purpose of obscuring the meaning".
Please note that this does not preclude the use of authentication (signed messages), were the message is sent "in the clear" with an attached hash (eg HMAC) where anyone can read the message, and can use your public key to verify that the message was signed with your private key, but only the holder of the private key (you) can generate the hash (signature).
My understanding is that the ban on encryption comes about from some countries concerns about spies masquerading as hams. If hams were permitted to send encrypted messages, then spies could pose as hams and exchange encrypted messages with HQ - this would probably result in some countries simply banning amateur radio, or banning their hams from communicating with other countries.