Shipyard capacity isn't a problem. I routinely build my ships bulky with 55+% engines. They're less capable than more compact designs and I may need 50% more ships, but they're correspondingly cheaper and faster to build. Total expenditure and build time for a fleet of a given capability is mostly unchanged (and I get fuel efficiency and redundancy for free).
In my opinion this is a problem with the current model of the drive systems in Aurora and one that most players don't realized yet.
It is by far smarter to use commercial engines in Military ships and just strap on twice the amount of them.
They use much, much less fuel which translate into a much smaller fuel industry needed, much cheaper to research, less crew and maintenance on ships. It is also much cheaper to build commercial jump drives to jump the fleet and require much less research in general.
The only real drawback is a larger heat signature if ships start to bloat in size but since the engines are so much cheaper then adding stealth also is much cheaper too.
In my opinion the game need a redesign in how engine, speed and fuel efficiency work. Military engines must be worthwhile to build on regular ships and not just on really fast ships.
First of all I would like to see a metric that make larger designs cost more the faster they go. Any form of maneuvering on a larger mass will become more stressful on the construction as a whole, there are no real mechanic to represent this.
There also need to be a mechanic that promote military drives and the importance of a larger mission tonnage per ship. Perhaps maintenance facilities could only service a certain size and total tonnage, this would promote more mission tonnage per ship. But it has to be more economical than the fuel you save.
Commercial drives could be more prone to explosions since they are not built for sustaining injury or have the same redundancy in protective systems. This means bigger drives that are easier to hit and will more easily injure a ship further.
I suppose there are other ways you can "fix" these problems. As said... from an economical standpoint military engines are almost pointless on ships from about 10.000 tons and up. Smaller ships still benefit from more powerful engines since there the stealth component is more important and you will need at least a decent mission tonnage part on those ships.