This is why I was suggesting once to have various different shipyards: each shipyard only builds certain units/components, just like in RTS-games.
We've got limited build slots per planet. What if, instead of upgrading shipyards, players constructed a piece of a shipyard into each slot.
Every shipyard piece would allow the construction of a few basic ship hulls with basic ship parts, increase the PP shipbuilding capacity of the planet, and charge a maintaince fee to local Industry.
Beyond that, each shipyard piece would unlock certain hull or ship parts for construction at that planet only. There'd also be an enhancement effect for stacking the same shipyard piece: if you build two Death Star Construction yards on a planet, then the Death Star hull would have more hitpoints when built at that specific planet.
Players would decide how to mix and match the shipyard pieces: Empire A might have a fast engine yard, stealth yard, and death star facility to build super fast invisible juggernaughts. Empire B builds three shield facilities for extra tough shields. Empire C builds his yards on different worlds, so that his expensive wonder-sized eggs aren't all in the same basket.
Could be other effects beyond unlocking ship parts. Maybe an extra capacity yard, a yard with a low maintaince fee, or an organic hull facility that eats Nutrients instead of Industry.