Well yes, you need someone to tell the ships what to attack, whether they are onboard or not. But if you assume they are not on board the ships, then you don't need crew compartments, as much hull space, etc., and the ships become more of a machine than a vehicle.
Basically, then, as long as you can communicate enough to tell them what your objectives are, and keep an occasionally updated algorithm for completing such objectives, you can just deploy them and have them do your bidding. Your ships can communicate among themselves faster and better than if you were to rely on voice-broadcast, and thus could coordinate attacks/defenses/strategies/tactics. Although some override for strategies and campaign objectives might be necessary, tactical command would be an unnecessary, and in some cases stupid tool. Computers could (if we knew how) be made much more effective at tactical/strategic thinking than humans.
Of course, it would be stupid to put the computers in charge of picking what an enemy is; if they detect hostility, they should merely defend themselves and make every effort to report back to human government/command for confirmation that they may engage.