FWIW, I also noticed that the basestars did not launch hundreds of raiders at once, but since the battles look awesome and busy and, most importantly, the game is fun to play, that's a plus in my book. Even more since I'm getting into single digit framerates territory in M6 already...
Even ignoring software and hardware limits and balancing issues, a battle involving hundreds of ships would make targeting an absolute mess. You'd almost have to limit targeting to ships that are directly relevant to the player's objective, turning the rest of the ships into background elements.
I'm just not sure how one could pull off that kind of battle in this type of game. Such is more the realm of strategy games and TV shows.
The key to targeting in that kind of battle:
1. Target under reticule. Always be able to target the ship you're looking at.
2. Good hotkeys for mission-critical targets (mission designer's job to do this, but definitely doable).
Honestly, the biggest bottlenecks to big battles are:
1. The engine's rendering not scaling well to lots of stuff on screen, especially if you include translucent missile trails.
2. Reaching the limits for the number of ships and weapon projectiles on screen.
3. Calculating collisions for everything in #2. This has come a long way, but it's still a quadratically scaling problem at heart, made worse by high-fidelity model geometry.
And the truth is, beyond a certain point, all of those extra ships present increasingly diminishing returns. I've made a few missions with 50 or a 100 fighters to a side, but they don't really feel THAT much bigger than ones with 25 to a side, especially after the initial clash.
Really, what makes a battle feel big isn't the number of ships involved as much as the density of the fight.
Urgh, sorry for the rambling. Can you tell this is something I've put a lot of thought and experimentation into over the years?