I think this is going to become difficult without breaking the conversation down into individual capabilities. First lets talk about a Drone vs a Flesh and Blood (Or
sentient robot) crew. In this case a drone will just be any small piece of hardware used to operate a thing. People could be
humans or sentient
robots... since a Sentient robot will require a decent enough amount of hardware to run on / support equipment / hardening / etc that they might as well be a
human anyways.
Drones vs People (vs Daqin)
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The biggest Drawback of using drones is that they can only do what they are programmed to do. They have limited decision making capabilities. This isn't an issue of you're something like a missile where your mission is very pre-defined and there aren't a lot of nebulous questions to consider. Similarly you also need to be flying something relatively simple since complex or creative questions around self-repair are going to be hard for a drone to solve. If you have a more complex mission to undertake, such as customs enforcement where you'll need to talk to people, investigate their cargo, or possibly be hit with complex questions you're going to want people. Of course you can use a hybrid model and have people operate drones remotely but that starts breaking down when light-speed lag is involved. Similarly if you need to repair and maintain equipment you're going to need someone there to do it in some capacity. You might be using a drone to change out engine parts in the reactor but if something complex comes up you're going to want a human there to troubleshoot.
The biggest upsides of drones are that they are lightweight, durable, and expendable. No one cares if a drone dies, you can always build more. Drones also are lightweight, in that the hardware to run a machine is going to be very small compared to all of the
life support requirements, cabin space, food, etc, needed for a human (or even sentient AI). Hardware is also a lot easier to harden than the human body. Sure it is expensive to build a motherboard that can survive 9G, but it is a lot MORE expensive to subject humans to 9G of acceleration.
There are some side benefits that also don't REALLY apply here. Without all the different variables of being in an atmosphere, calculating ballistics trajectory is a lot easier. Drones would have perfect accuracy when shooting and humans would not... but humans wouldn't really be aiming guns on ships in the future anymore than they do today. They would pick out a target and the fire control
system would handle the shooting. When it comes to mechanical tasks like that I don't think humans are really at any disadvantage there.
Drones
+ Can more easily handled high Gs long term
+ No one cares if they die
+ Far lighter-weight than having a crew
- Can only do what it already knows how to do
- Anything fun you want to do requires people
People
+ Can handle complex tasks that require creative thinking
+ Anything fun you want to do requires people
- Easily killed
- Can't handle High G
- Expensive
- Requires lots of heavy equipment to keep alive long term
Now lets consider the Daqin. They are somewhere between Drones and People. They can handle complex tasks that require creative thinking, but they don't have the same requirements for keeping them alive in space. Instead of needing all sorts of equipment, they can put their body into stasis in some G-reducing breathable liquid and have their mind run the ship in VR. This is certainly heavy and expensive but not nearly as much as people. You don't need nearly as much life support, radiation protection, food, creature comforts, etc.
Daqin
+ Can handle complex tasks that require creative thinking
+ Anything fun you want to do requires people
+ lighter-weight than having a crew
+ Can handle High Gs long term
- Expensive
- Requires heavy equipment to keep them alive
While there are still drawbacks to using a Daqin on a spacecraft, there are far fewer drawbacks when compared to Humans. While I don't think you would put a Daqin on a missile, I do think you would see Daqin employing smaller craft than humans if for no reason other than the Daqin just need less space for their crew. Daqin will also be able to handle high Gs far better than Humans, so I would also expect Daqin ships to be faster than Human ships across the board as human ships are far more limited by G-forces. If you need a fighter (Or small attack ship) that can accelerate at high G for interception or avoiding attack then as a human you MUST use a drone just because you have no other choice. If you're building a fighter as a Daqin you don't have that limitation.
Small Ships vs Big Ships
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There are a few things that dictate ship size, and in some situations 'fighter' sized craft just absolutely won't work.
Mission
What are you out there to do? For transporting large amounts of cargo you just can't use a fighter because you need to be able to move a large amount of heavy stuff, and even if your fighter has great power to weight you're still limited by your small engine. If you're attacking a starship, you're going to need
weapons that can deal damage to it. I would think for classic space-opera style fleet battles out in deep space you are going to need large weapons. Your ship can only be as small as the equipment you need to carry so there is a lower limit to how small you can make things.
Square Cube Law
This cuts both ways. Internal Volume increases faster than surface area. This means for the same thickness of armor, your armor is going to weigh less as a % of your ship's total weight as you increase your ship's size. Similarly, there are some benefits for going bigger that scale the same way. It takes the same amount of space and weight to house a single human regardless of the size of the ship. That means all other things equal a larger ship is going to be weighed down less by its communications gear, control systems, etc, than a smaller ship.
Inertia
On the other end, you're going to need more structural support for a larger ship just to hold the engines in place. Fast maneuvering is going to require a very strong ship, and it is harder to maneuver fast without tearing yourself apart as you get bigger. Sure your straight line speed will probably be better than a fighter (especially long term), but you're going to have a hard time with precise movements.
Cost/Numbers
While you could build one large ship that is objectively better in every way than two smaller ships, that one ship can only be in one place at a time. It can only protect one location, or intercept one ship at a time.
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So when designing a ship you're going to have to think about all of the above. You're not going to get the same dynamic of fighters vs battleships simply because the battleships in this analogy would also be able to fly. Instead you'd be designing the smallest ship you can that will still carry everything you need to do your mission.