AFAIK, Automerge people work pretty hard on Beehive and Keyhive. Once released, that’ll be exactly what you asked for: https://www.inkandswitch.com/keyhive/notebook/05/ You can also use Yjs over Matrix (which has e2e encryption): https://github.com/YousefED/Matrix-CRDT

another shameless plug: there is NextGraph.org which does exactly tha: E2EE CRDTs. It supports Automerge and Yjs (and soon Loro). It is being used already by several apps. The SDK will be released in November. Stay tuned by following us on https://fosstodon.org/@nextgraph and subscribing to our mailinglist https://nextgraph.org/

In theory, you can exchange CRDT update information over any channel you like (say, MLS) https://martin.kleppmann.com/2019/05/15/encrypted-crdts.html

You mean something like this? https://jakelazaroff.com/words/homomorphically-encrypted-crd...

It is slow and inefficient, but can be done.

Fireproof implements a CRDT and implements E2E. https://use-fireproof.com/docs/welcome/