I am using Devonthink on Macs and 2 iPads. Since the iPads and one Mac are not in the same iCloud (for work i have another Apple-ID) I have to use Dropbox to sync.
When I annotate a PDF on the iPad, it does not sync to the other iPad.
But a test with a sync via iCloud (Cloudkit) shows that it works fine with iCloud.
I find synching on iPads slower than on Mac. I guess make sure that you leave enough time on both iPads to complete the sync with Dropbox and Mac (three devices involved, and my hunch is that DEVONthink does not do them in parallel but serially).
Perhaps also add Bonjour to the sync locations and run both Bonjour (which will be reliable and fast, but requires the devices to be on the local network) and Dropbox.