Do all the other teams have same size hit box? I don't get why only one has a different size.
Yes all the other teams have the same hitbox. Only Yukari and Reimu have different ones. It has different size due to different attributes for the characters. Like Youmu has only half of an Imperishable Night (what was it...) bar and Marisa has auto collect if she goes to the top of the screen and Sakuya slows down the items falling from the screen. See to break it down simply;
Reimu: Easiest to use, mostly for just completing the game.
Marisa: Somewhat fast high attack power auto collect for items. Most likely if you want points.
Sakuya: Fast and you use her for points.
Youmu: VERY FAST high attack power. Mainly to finish the game, like Reimu.