I'm not so sure if ComStar is the party to handle encryption.
The service ComStar provides is "jumping" the transmitter signal from a HPG to its destination - usually another HPG, but potentially any place anywhere where they expect a receiver to be nearby.
(HPGs do have "receiver" rooms but their purpose is to dampen the signal so that it doesn't cause damage via its emergence wave and cannot be listened to; also it is possible, but wasn't spelled out anywhere afaik, that some sort of receiver antenna is required within a gravity well.)
In any case, that says little about the message itself. You can apparently deliver a message to a ComStar temple in a myriad of ways, even show up personally to record a message or have it written down by Acolytes. Presumably, ComStar dicated messages to be delivered open and unencrypted prior to the 3050s simply because they could, and it helped ROM stay on top of what was going on. Mystic mumbo-jumbo was used to explain the requirement.
There was no need nor even a desire for encryption, as all message traffic was handled within ComStar.
This is the timeframe where WolfNet was most successful.
After the schism and as HPG technology proliferated to other factions, it is reasonable to assume that you could deliver data storage devices that held encrypted data, and have these transmitted as-is. The trust in ComStar was largely gone, and most nations were already using alternate channels for top-secret data, and had been doing that since before the 4th SW. But like in the real world, if secure channels are too cumbersome to use some people will revert to the internet...
Another thing is that I've long suspected Wolf's Dragoons have been using at least one Bug-Eye surveillance ship. I seem to recall a single one was even mentioned somewhere, but I can't find the reference.