so 2-3 fighter squadrons, 5-6 bomber squadrons, assuming the default 8 squadrons?
I think 3-5 or 4-4 work well for the following reasons: bombers can cause a maximum of 3 hits, plus +1 max per each bomber squadron after the first one (each one also gives +5 to the bombing run test). When escorting bombers, each fighter squadron causes -10 BS to the enemy's turrets attempts at shooting down the small craft (Crew Rating + 5 per turret rating). So:
1 - A run of 5 bomber squadrons escorted by 3 fighter squadrons can cause a maximum of 7 hits with a success +6 DoS (7d10+28 - enemy's weakest armor = total dmg), and enemy turrets firing at them will take -30 BS. If the enemy crew rating is 30 and they have 2 turret rating (most cruisers), they'll be rolling against 40-30 = 10% chance. Low chance but just a single success already takes down an entire squadron and not just a single craft, mind you.
2 - A run of 4 bomber squadrons escorted by 4 fighter squadrons can cause a maximum of 6 hits with a success +5 DoS (6d10+24 - enemy's weakest armor = total dmg), and enemy turrets firing at them will take -40 BS. If the enemy crew rating is 30 and they have 2 turret rating (most cruisers), they'll be rolling against 40-40 = 0% and auto-fail, meaning ships with less training/defenses will get pummeled unless they have fighters of their own to intercept our squadrons. Even if their CR is 40 and they have 1 turret rating (experienced pirates in a raider or frigate for example), they'll be rolling against 5%. For the chances to go back to 10% would require a cruiser with a Crack crew.
After doing the numbers I think I'm leaning towards the second option because while the ceiling for damage is lowered a bit, Marco would need to roll very well to make usage of that ceiling anyway, and having enough fighters screening means not having to worry about craft losses unless the enemies are harder to crack. Lowering our chances of losing entire squadrons might trump losing out on a bit of damage in case we get a very lucky hit.
As the game progresses we might decide whether to skew the rates or even whether to amass larger strikes by having the craft loiter and wait for another batch to be catapulted out of the carrier for example (for a total of 16 squadrons).
Counterpoint, boarding craft means more loot. Pillage, THEN burn.
The best way to capture a ship with as less damage as possible is via boarding since that way you can choose between causing damage to the enemy ship's hull or just to its Pop + Morale. That sort of action favors having troops (like from a Barracks) and being fast enough to end our movement turn within 1 VU of the enemy to initiate boarding. Or being specialized in boarding and having a harpoon-gun macrobattery.
Hit-and-run attacks are lightning raids and have extra steps to cause damage so it's usually better to focus on them only if you have something that'd give you an overwhelming advantage like barracks full of troops, murder-servitors, a teleportarium and so on. They also cause hull integrity damage, and their main real usage is causing critical hits to cripple the enemy ship. Murder-servitors help because you can pick a critical between 1 and 6 instead of rolling 1d5.