Should you catch raquaza with a masterball?

You can if you want you don't have to. Rayquaza is a dragon type so if you hit it with ice moves like Kyogre or Walwrin it shouldn't be too hard, but you'll need lots of Ultra Balls and alot of patience and make sure that you save before you battle him just in case, but if you want to do it without trying to hard just use the master ball.