===== Why do I have (insert number) cruise missiles in a particular Air Unit, but that Air Unit fires (insert greater number) cruise missiles during the campaign =====

Incomplete. It may be useful to think of a cruise missile as a platform which delivers an SCL (the warhead). In that context, the number of missile “bodies” authorized/on hand (as with number of aircraft assets) together with sortie rate governs the number of sorties per day, whereas the number of warheads on hand governs the total quantity of cruise missiles available to expend. Decrementing cruise missile bodies, then, would be like decrementing (reusable) aircraft rather than (expendable) SCLs.

Cruise missiles don’t consume the air asset “cruise missile”, or decrement them as a result of them being used in a previous ATO cycle or currently flying--as set by the “Is Cruise Missile” flag. The quantity authorized/on hand is used (along with the sortie rate) to determine the number of sorties that can be launched in a cycle. The warheads (AmmoAir genre) are the consumables (think of them as the SCL for the Platform “cruise missile”). Total cruise missile inventory is controlled by limiting the warheads--which can be replenish by supply. 
