I had a strong suspicion that the firmware was the culprit. The DNS-320 and DNS-325 were released around the same time as the DNS-345, and both NAS required firmware updates to fully support 3TB HDDs.
One issue of concern is the fact that you upgraded your firmware with the EU version, which was designed for hardware manufactured in that region. Please see the following thread:
DNS-345 - Firmware Do's and Don'ts.
I'll leave it up to you whether you want to downgrade to the latest AU firmware or stick with the EU version. I don't have enough information to determine if the firmware you selected is fully compatible with your hardware or wil be stable long term. From what I know about firmware updates on the ShareCenter series, changing the firmware version should not impact any previously formatted HDDs.
There should be a method to add additional HDDs, but unfortunately I don't have access to the firmware or a firmware emulator for the DNS-345 to offer the proper procedure. Based on my reading of the manual, the "Hard Drive Configuration Wizard" should provide you with the option of formatting just the new HDDs versus all installed HDDs. This is something you'll have to test on your own.