Ill bring this up, for now a work around would be to use the automation feature to set all idle shipyards to build a specific ship
I have never had the shipyard open auto unless I clicked tab or the icon in bottom right, also have never had the shipyard not be in the GNN, just need to select the shipyard/s that have finished building a ship.
That said there is a Major Flaw in the UI that clicking on the shipyard using tab or the icon does not center the map on the shipyard. Selecting a SY from the GNN does center it on the map.