If the place is warded against teleportation, is it also warded against planar travel? That would prevent the night hag from going ethereal in the first place, which might explain the "third hag begs for her life" encounter advice.
The adventure has a chart of wich spells & effects are altered & their results.
Straight from the adventure:
"Etherealness The caster enters the Border Ethereal but can't move through surfaces or doors in the tomb. Ethereal characters might encounter one or more of the Sewn Sisters."
The Sewn Sisters are the hags being discussed.
It also goes on to specify that the alterations do not apply to Acererak himself. Wich leads me to remind you that....
In any adventure of any edition, it is a grave error to assume that what affects the PCs one way also affects the villains in the same manner.
In case you've never noticed, NPCs often manage feats of magic the PCs can't even begin to match. Ex: Any flying castle, the ToA, etc.
If you want a climactic final battle, let the PCs take a full long rest, and then up the difficulty of the bad guys. How many simulacrums can Acererak deploy at one time? Maybe double the Atropal's damage across the board?
Having just finished running this, none of that'll (likely) be necessary.
*Follow the rules for movement, concentration, etc.
*Play the atropal & Acererak
SMART - they're INT.25 & 27 respectively....
*Study Acereraks listed spells & items carefully & use them well.
*You know that hag? If she cuts a deal with the party there's a curse effect that'll hit them if they then attack her.
I had her enter the room (to spectate) while the party was fighting the atropal/Acererak. One of the players assumed she was up to no good &, encouraged by several others, attacked her.... The curse then triggered on all 3 of them - auto-fail save vs Contagion & immediately contract Slimy Doom.
The only thing you might do is up the Atropals HP. I had a ranger, barbarian/monk, & fighter/rogue in the party that were very good at pumping out the damage. So I rarely ever used the listed average. Often 85%-100% HP for things.