I like the idea.
In order to address the time-of-builds issue and stop capital ships spewing out dozens of craft per minute, perhaps require the number of blocks and their placement to define effectiveness. i.e. If you place an L shape of 3x3x3 (a la power cores), it produces 9 blocks per 5 seconds or something. And they all have to link to a 'shipyard mainframe' computer block.
Another mechanism to limit production would be using docking/turret enhancer style placement of the shipyard blocks, to control the maximum dimensions of the ships produced, preventing a little frigate from launching Titans!!
(Also, I think the ideas could be merged - to control time and space!)
Those are two ideas anyway, that's a penny each.
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Horrible idea ever, i see massive ships building a stupid drone numbers on the go while fighthing other ships, however if the ships that build ships cant be used properly for combat situation would be nice.
I had a similar concept on a fleet I designed for a story. It was designed to be a long range, self sufficient fleet and had mining ships and what I called forge ships, which were extremely lightly armed, and just processed all the materials the mining vessels captured. Mine were only producing munitions and replacement hull plates, but the idea is the same.