Add a few random, un-lootable, pieces of clothing to the NPCs that load up and throw on disguises. The disguised NPCs have already done a ton of good for the small-world problem of everyone knowing who the shrouded average playa is, but as it stands right now when a masked/hooded one walks in you can tell they are an NPC as soon as you look at them because of their lack of shoes/pants/etc.
I think a simple fix is to just have them spawn with non-lootable depot clothes, du-wear, topside clothes, and maybe a naked or two to make them blend even more.
GATO