I -can- see where a mission with a bunch of random explosions and stuff seems really neat, and all -- but to be honest, unless it's a cinematic where the player is AI locked to do waypoints, The number of ships have to be coordinated all together, and the more ships you have the more co-ordination.
Combat missions usually involve sparse fights, and a realistic armada would not be clashing heads with a huge fleet. If you are doing a mission with a massive train of ships (i.e. Battlestar Galactica and the many ships that are about) would be better to do a Hi-res rendition of the armada majority, and make it a part of the background. Or if you actually did it, you'd have to make sure all the ships are constanttly acting independently to make sure they don't collide.