I've been watching closely at how the Master Logistician works for supply savings and I can't see any difference between when I have one in a big army or take him out. In fact I have tested this by having big armies with a Master Logistican in it and noting it's supply usage and then taking him out and running a turn and seeing the exact same supply usage numbers.
From my tests I have concluded that either the Master Logistician's supply savings does not work or else it somehow works "behind the scenes" and we can never figure out if it works or not. I would hope that having a Master Logistician in an army would show us that supply savings as we put him in or take him out of an army and we could see it as he goes in or out right away.
Omnius