TWR isn't the only thing, structural integrity needs to be considered too.In space its all about a ship's TWR (Thrust to Weight Ratio), there's no drag to get in the way, not on any noticeable level anyway. Sure large warships are heavy, but they also have large propulsion units to counteract their mass, which should result in decent rates of acceleration for warships.
Awesome acceleration doesn't help much if the ship breaks apart because of it.