The Amateur Radio Service and encryption
The Amateur Radio service is a public asset which requires one to be licensed in order to legally transmit using the Amateur Radio service assigned radio frequencies (RF). As a public asset, the Amateur Radio service cannot expect any privacy. The Part 97 rules make this aspect crystal clear. The rules have many references to "... the purpose of obscuring ..."
Encryption is a method of encoding data so as to obscure the content of the data except to the selected audience. Part 97 does allow encryption of control data. Control data is not considered a "message". Examples given in Part 97 are control of RC models (97.215) as well as telecommands to space equipment (97.211).
Data transmission on a Part 97 RF network, like Broadband Hamnet, which employs encryption with the intent/purpose that only the sender and a select receiver can decode the message (and nobody else) would be considered a violation 97.113(4). The key word thoughout Part 97 rules is purpose. This rule is not regulating the method, only the purpose. The Broadband Hamnet site has a reprint of an article which delves into this issue: Data Encryption is Legal
When we look at other paragraphs in Part 97, we can see an implied exception to transmitting data where the message is not initially clear. In 97.309(a)(4), we see "... any technique whose technical characteristics have been documented publicly ...". And in 97.309(b), we see "... data emissions using unspecified digital codes must not be transmitted for the purpose of obscuring the meaning of any communication". Again, the key word of purpose is present. The rule is not dictating that unspecified digitals codes cannot be transmitted. It just says that you cannot transmit with the purpose of obscuring your message.
So, under what purpose would encryption be acceptable? Believe it or not, Part 97.113(c) gives us the answer: "No station shall retransmit programs or signals emanating from any type of radio station other than an amateur station". The 2.4 Ghz and 5.8 Ghz bands are shared with Part 15 devices. Encryption with the purpose of preventing the "retransmit .... signals emanating from any type of radio station" would comply with 97.113(c). And taking a clue from 97.309(a)(4), the technical characteristics would need to be documented publicly (ie. the use of WEP or WPA). And it would also be prudent to have the messages and key available for inspection should the FCC come knocking.