Wing Commander CIC

After each mission, you get an e-mail within the game stating how many of each fighter type the carrier has remaining. At least this started with episode 2. What is the signifigance of this? If I waste all of my Stilletos (which I only have 6 left last I looked) does the game have me fly in something else? Also, is there a place that I can choose my ship before the mission or is it done for me most of the time? The only mission that I got to choose my ship was where I went after the girl that took off in a Sabre who defected. (I can't remember her name now.)