If Ao would have a grudge against Dead Three, he wouldn't send anyone to solve it. He would just outright DELETE all of them.
(And Vlaakith not even a real goddess). In reality of Forgotten Realms that plainly means her name is not in Ao's Tablets of Fate.

Also Larian's pull that mindflayers supposedly soulless just goes against the lore. Neither spellcaster, nor psionics could be soulless. Soulless constructs can be infused with some magic, but in order to actually cast a spell or manifest psionic powers - having a soul is actually a main "component".
So, both mindflayers and elder brains clearly have souls. They might not have their souls circulate normally as other mortal souls do - but souls they do have. Cannot not have those.