I was suggesting once to have various different shipyards: each shipyard only builds certain units/components, just like in RTS-games. This takes care of "captured-shipyard-problem": sure you can use all your resources to pump out ships at the captured yard, but all you will have is masses of slow short-ranged behemoths, getting picked off by the long range fighters that your opponent built meanwhile. If we really have unlimited shipyard production, this would be a nice way to balance it.
I dunno... that depends on the enemy having lots of specialized shipyards set up with the perfect counter to the one you've built. If you also happen to have brought along something that counters what counters what's built at the shipyard you captured, there's still a problem. (... then again, maybe that's a good strategy to retain?)
I don't imagine many people will want to make shipyards that specialized either. If, surprisingly, unlimited pooling is adopted, I imagine most won't want to have some other reason they have to build a whole bunch of separate shipyards.
Also, does a shipyard only build a single hull, and any kind of weapon, or only a single kind of hull and a single kind of weapon... (ie each shipyard is specialized to a particular ship design)? If weapons are part of the ship balancing, which I'd like, then you'd need to limit which shipyards can build which. If you do this, then you'd have to go with multiple shipyards per system, which would just be like the addons method, or limit a shipyard to a particular ship design only, which is waaaay to restrictive, I imagine.