If the world was static, all problems would be gone. But just as there are small outbreaks e.g., of smallpox, etc., things change over time and problems can resurface. Dropbox isn’t sitting still and neither are we, developmentally. Just look at the Crowdstrike debacle going on. Innocuous update, right? Seemingly, and with far more disastrous results than a duplicated document here and there 
The problem would go away if I were to turn off “Synchronize contents of indexed items”. The manual suggests that as a space saving measure. Unfortunately, the manual also says that one shouldn’t do that if using DEVONthink To Go, since the content in the synchronized databases is the only content it has access to.
That is correct, re: DEVONthink To Go. Even if you weren’t using a shallow sync, the contents need to be available in the sync location for it to transmit data between it and a remote sync location… which leads me to: Why are you using a remote sync option at all? To beat the deceased equine once more:
Regarding syncing, the first question you need to ask yourself is, “Do I need a remote sync option?”. Consider these questions…
- Do you need to sync between machines – especially non-portable desktop Macs – in different geographic locations?
- Do you have a colleague, assistant, significant other, etc. that needs frequent updates to synced data?
- Do you need to use a shallow sync, i.e., Download Files: On demand in DEVONthink To Go?
If the answer is no to any of these questions, a local sync on your network is suggested.
There is a forum post on syncing: Sync Types Explained. This is a good place to start.
There is also one specifically about Bonjour: Bonjour Simplified
If nothing else, I would disable the remote syncs and try the Bonjour sync on your local network to see if the duplication persists. I have a suspicion it won’t, but that’s what the scientific method is for
PS: See my response to your support ticket before proceeding.