It's rather unrealistc to have a pilot that can fly any aircraft, because of the differences between types. If a pilot switches types, they have to go on an orientation course to get to know the aircraft before they can fly it well (if at all). So unless FS-era fighters and bombers all have a standard cockpit suite, then you'd have to have pilots trained for each type.
I think that FS squadrons have a pool of craft of different types, so that they can fly whatever's best depending on the mission. So a fighter squadron would have Myrmidons, Perseus and Herc 2s, a bomber squadron would have Artemis and Boanerges, and an assault squadron would have Herc 2s and Ares, as well as Artemis bombers. You'd also have "specialist" squadrons, that specialise with one type, and "elite" units may have a wider range available to them than standard.
Overall, I'd guess there would be something like a 3 - 1 ship/pilot ratio, though it would fluctuate somewhat.
One other thing to note is the specialised nature of vessels in FS. Fighters are only useful as fighters, bombers aren't much good at anything else, recon ships are useless in a fight, etc. That's very different from today's multi-role aircraft that can do pretty much anything (the Super Hornet and the Typhoon are excellent examples of this) if they are carrying the right weapons. It's more like the situation in the Second World War, with specialised types for each role.