There are a few shortcuts with joystick controls worth mentioning. There may be others but the ones I use are:-
double tap button two to afterburner (hold down on second tap).
increase/decrease speed by holding button two and moving forward/back
roll ship by holding button 2 and turning left/right
fire missile by holding button 2, then pressing 1.
Alt-B will order your wingman to break and attack without having to go through the comms menu.
One other thing worth mentioning is that Wing Commander has a branching mission structure depending on success/failure. You don’t have to win every mission to beat the game and you will get sent down different mission/story paths if you fail. You won’t see half the missions in the game in one playthrough and there is a strong case for living with your failures and seeing where you end up. The sequels largely dropped this feature as most people just reloaded if they failed a mission.