If I command a fanatic NPC it looks like I get a +5 bonus per success level to skills. Does this bonus work for shooting/ballistic tests?
In The Inquisitor's Handbook, on page 227, it says that a successful Command Test will
grant a +5 bonus on a single Test related to that order for every degree of success attained.
With this in mind, as long as your Command has something to do with shooting, I would rule that it absolutely applies to Ballistic Skill Tests.