Yeah I 100% agree with this.
Now I don't ever see the need of putting my own shipyards on repeat so I stop getting popups, but I do think it should be an option. The research one imho is the only one worth doing ... if you can pay the promethion cost. For context though I usually have no more than a dozen shipyards and play with Large, Many sectors. Most game end around turn 150 but i did push through a conquest victory to 250's recently.
I personally just setup Rally points and never stop building ships....but thats because maintenance might as well not be a thing. Think I had 30 BC maintenance for my last playthrough with over 60,000 military score. I wouldn't mind seeing maintenance force the player to actually pay attention to their income and counter the mid-late game income generation.