Makes sense to me, thank you for pointing this out.The decision for ix-applications to be created unencrypted was intentional:
https://github.com/truenas/middleware/pull/9954
Bottom line is, ZFS encryption should be used for pretty static datasets. It's not great for parent datasets where lots of dynamic datasets are coming and going frequently, which is the case for ix-applications due to how containers are checked out and snapped.
I saw the actual issue (warning generated, even though it works as intended) already has a PR. Thanks for resolving this minor annoyance quickly!