Your link isn't arguing that encryption being prohibited is silly, it's arguing that proprietary protocols like D-STAR are effectively "intended to obscure the meaning of the communication" (for profit rather than secrecy) and shouldn't be allowed.
My understanding was under one interpretation encryption was always permitted by the FCC on ham bands over 50mhz but by a 2:1 majority common wisdom within the community (and the ARRL itself) hadn't come around to this line or reasoning[1]. Specifically encryption is not allowed if it's "for obscuring meaning except for the following circumstances" of which authentication and securing network operations are two. I would want some legal precedent or an amendment to the code before weighing on this too heavily to see which of the two interpretations takes priority.
That article isn't the final word but it's interesting following the work of the broadband-hamnet folks - particularly in Texas[2]. They mostly say one can't use encrypted traffic. They are however relaying IP traffic but imply one shouldn't use https.
During National Emergencies (like now?) a lot of the rules around call signs, power, and presumably encryption fall by the wayside. In practice it looks like the FCC grants per disaster waivers[3].
