A hitbox is the area of an object used to determine collisions. In danmaku games, these are traditionally smaller than the actual image, in order to allow the player to dodge dense patterns.
The bullets have various hitboxes, the general rule being that larger bullets have a smaller ratio of hitbox to image than small bullets (i.e., the larger the bullet, the larger its "safe area" is). In addition, many of the bosses have hitboxes larger than it would appear, allowing the player to hit them more easily.
Delving further into specifics, the general size of a Touhou character's hitbox is around 5 pixels in diameter. Starting in Perfect Cherry Blossom, Reimu traditionally has a smaller hitbox, measuring about 4 pixels in diameter.
Even without going into focused mode, however, it is generally possible (and quite easy once you get the hang of it) to give a decent approximation of a hit box's size and location by taking a look at the characters; usually, a small design on their clothing around the character's waist usually can point out where it is.
Additionally, a snowflake or spell circle will also surround the character. These represent the graze hitbox and the item collection hitbox, respectively.