Unfortunately no, the only custom-kitted NPC I've found that has HLAs is Minerva at artisans-corner.com. The Icewind Dale NPC mod NPCs at pocketplane.net have them, but those are stock kits. Dusky and Dandjelion at weaselmods.com also have them and are stock kits. The ones I've confirmed do not are:
artisans-corner:
Karihi - Pyromancer, Mage
weaselmods:
Orra - Fighter/Mage/Saishi, Fighter/Mage/Cleric
L'anna - Mythseeker of Mythrien Sarath, Paladin
Hommet - Deadly Blazing Necromancer, Mage
Urchin - Don't know this one, I don't have a save with him in my party and what I think is his kit in EEKeeper just says L#URCH.. iirc from when I edited him once his class was Hag Abomination or something, not even a stock class. Could be wrong
I haven't tested the other NPCs from weaselmods, but most of them are also custom kits.
I remember from awhile back when I was playing EET with Skills and Abilities, the new HLAs like Great Charisma etc. did not work on the custom kits from Might and Guile and other such mods, which is what led me to believe they were added per-kit. I haven't tried them in EET in several months.
I'm not a modder by any means so it's just conjecture on my part
I really appreciate the mod though, I couldn't live without it anymore.