An interesting find, I think. I'm amazed there has been no similar topic. This is what I'd like to share with you:
During my latest run with an assassin charname in BG2:EE with the SCS mod installed I've just completed the Find evidence against Mae'Var quest.
The 6th stage of this quest is the Elimination of Mae'Var's guild. According to various resources (http://www.sorcerers.net/Games/BG2/Walkthrough2/SoA/chapter-2/quests/class-thief-find-evidence-against-maevar.php
and to my memory as well, one could always find the Shadow Armor on the Mae'Var's coupse.
But for me it wasn't the case. No Shadow Armor dropped by Mae'Var.
This problem is also mentioned by @Pblack
) and is discussed here: http://forums.gibberlings3.net/index.php?showtopic=26322
I have no mods except the SCS installed but it seems this mod has nothing to do with the Shadow Armor. So, this seems to be a change in BG2:EE.
Not a big deal, of course, because the Nights Gift +5 (AC 3, +20% to Hide in Shadows) that is given by Minister Lloyd in the Mayor's House in the Umar Hills after the Deaths in the Umar Hills quest, is better than the Shadow Armor (AC 4, +15% Hide in Shadows).
P.S. Also, although Renal Bloodscalp gave me 10,500 GP and offered me to take over the Mae'Var's guild, he didn't give me the Short Sword of Backstabbing.
P.P.S. I'm currently a little bit away from my usual activity here but I've been able to play BG a little bit and thought I should share this with all of you.