I imagine that the individual ships themselves will also be very small. In fact, if a fleet is big enough, the communications gap becomes a problem - space battles may end up looking like a fight between two ant colonies, with small independent ships working together as a swarm, without any central guidance.
You never know. I'm sure you could have a more "distributed leadership". I'm sure this could be accomplished with a clever enough application of paxos.
I agree with the author in that it's unlikely we'll get a Star Trek scenario where a single ship can continue taking hits without much consequence. In all likelihood the first hit a spacecraft takes will destroy it.
In that environment you really want as many small ships as possible - large capital ships really work against you. Any centralized command system would also be trivially easy to destroy by concentrating fire on the command ship.
A swarm of distributed ships seems much more viable in this system.
