This is what I do
Use the "PLANET" the "PLANET SY" and the "SHIP SY" buttons to make 2 or 3 separete construction queues.
For planets without shipyards, first sort by number of facilities, then by construction queue.
You then get a nice readable list of planets.
For planets with shipyards, I either do as above or first by name, then by construction queue.
I also usually rename Base shipyards to their system name to get them listed properly.
This works OK even in very large games like the aptly named "Return to Hell" game on PBW where I currently run 750 planets and 1800 Base shipyards.