You're not entirely wrong, an undocumented plaintext protocol is functionally not much different from encryption.
However, those which are legitimate (ie, just undocumented, not intentionally encrypted/obfuscated) don't tend to cause problems as only one or few ham devs would be using them. They can only get widespread adoption by other hams if they are documented. So this regulates itself.
A corporation, on the other hand, is not like some ham dev coming up with their own protocol. They can design their own protocol, and then roll it out on thousands (or much more) of transmitters. So just one corporation can cause quite a big problem, with zero public documentation.
The laws as they are, together with direction finding skills, are the communities only (legal) tool to defend against that.
That does not mean hams don't see the value in encryption. I do! But it's a trade-off, and I think this is the only way it can work. The legal change I would like to see is explicitly allowing cryptographic signatures. Right now it's a grey area (likely legal, but not court tested)