I did the Counting House last night.
Tav has the "See Invisibility" buff from Volo's Ersatz Eye. I noticed that many of the invisible NPCs weren't showing up. My suspicion is that the enemies were using stealth in addition to invisibility, making it more difficult to reveal them. Some Area of Effect spells, grenades, and Cleaves without targets worked well to reveal the hidden assailants. The guards were also revealing some of the invisible NPCs, though not often. The fight can be frustrating, especially since they seem to pop up all over the map.
I hope that helps. Good luck!