For anyone that cares here is the ubisoft response stating that achievements are going to effectively stay broken in the connect launcher :
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In reply to the two issues that you have listed, I apologize if this was not made clear before, we are aware of both of these issues through the player feedback we have received >
Issue 1 > Notifications not being displayed when an achievement has been completed
Issue 2 > Players requesting the Achievements section to be accessible from the in-game overlay.
We do have a new update to share however - The decision was made by the Connect team to keep notifications disabled and from popping up when an achievement is gained. The same applies to the achievements not being visible in Connect when in-game.
The reasons made to remove these features are not known to us, we do not have visibility of why this decision was made, but we continue to pass reports on from our forums, to our Connect team, to show how players would like both of these features added to the launcher in a future update.
We do have a new update to share however - The decision was made by the Connect team to keep notifications disabled and from popping up when an achievement is gained. The same applies to the achievements not being visible in Connect when in-game.
The reasons made to remove these features are not known to us, we do not have visibility of why this decision was made, but we continue to pass reports on from our forums, to our Connect team, to show how players would like both of these features added to the launcher in a future update. "
So stupid! Shame on Ubisoft developers.