From the OmniFocus blog:
But, with our latest updates today (OmniFocus 2.6 for Mac and OmniFocus 2.15 for iOS), your data will be completely encrypted before it leaves your device so that it’s encrypted on the server itself.
This is a major improvement for me. I've always given the OmniSync server a side-eye for tracking tasks with sensitive information in them. This was especially true of tracking work tasks. With device-side encryption we're getting closer to my ideal. The latest Omni updates have really focused on solving some complex problems for their highest level users. Kudos to them on this step.