The theory you just described above is one that has been around for quite a while. In Everquest, we said named mobs (the equivalant to NM) had "placeholders". Basically, in a given area, room, or zone, mobs of one type spawn at a certain spot, and the named mobs had a small chance of spawning instead of the placeholder mob. Even in a case of multiple types of mobs having the possibility of spawning in one spot, it would go something like this:
Time for mob to spawn (depends on the "respawn" time of the zone, area, etc).
X percentage of mob A.
Y percentage of mob B.
Z percentage of mob C.
If mob B is supposed to spawn, D percentage change of NM spawning instead.
As to your theory about the moon phases or days, I say its a pretty good one, considering how tradeskills in general and also the HQ item successes are also highly tied into the day of week and phase of the moon.
If the drop theory mirrors the HQ item theory, an increased chance of spawn might occur the day BEFORE the one of the crystal the mob drops.
Very interesting subject matter.