To the initial premise of fighting a war with unmanned starships rather than manned starships given the high level of computer technology in the future.
It would seem that this type of warfare would be the most likely evolution but it makes for poor fiction. Computers could easily be programmed to recognize and react to hostile targets, communicate with other unmanned forces and engage in combat appropriately. It clearly sanitizes war . . . at least until some unmanned forces come into contact with manned vessels or planets . . . in which case it depends on the programming as to what happens then.
As an economic power the Federation would seem much more productive in mass producing unmanned ships and computer programs than training sentient beings to go into space to likely be killed in combat. It would seem a FAR more productive form of warfare for the Federation (or most races really).