Currently available in NV2 to prevent duplicates is the F3 key on the Reference field to allow you to take the Next Reference Number based on the journals next reference.

To review if duplicates reference numbers exist, click on the reference title which will sort the posting/transaction explorer by reference (note the cevron (v)) number order.

What if in the journal a journal option was added (under Sub Journals) whereby you could specify to Disallow Duplicates as a Yes or No?