For Magic Carpet, I didn't even think about playing it with anything but mouse+keyboard. Getting used to the flying carpet "physics" should be quick, and given the speed of the game, aiming with the mouse makes things easier. And, well, a joystick makes sense for a ship, but as feeling goes, it's not particularly fit to a carpet!
As to other simulations, you should indeed get a joystick, or a pad. Sure, you will have to deal with some issues here and there (depending on the type of support for them in old games), but it's worth it. Freespace is playable with the mouse, but the feeling will still be odd. X-Wing and TIE-Fighter were meant for joystick much more than anything else. For the Descent series though, the mouse is really OK, as the ship behaviour is meant to react only to small movements of the mouse (kind of simulates the weight - do as if you were turning your head and the ship will stand still). I finished the 3d one with this, and had a great time and satisfying flying sensations.