It might be good to clarify some terminology around the "holes". There are often two sets of similar holes punched into revenue stamps of this era:
Perfins to ID the owner and protect from theft, misuse, etc., just like with postage stamps.
Punched cancels which do exactly that, they cancel the stamps, often tying them to the document simultaneously.
As an example, here are two images of the front and back sides of a document with revenue stamps on the back.


Back-lighting the two NY state stamps on the back shows the "J&Co" perfin holes of Josephthal & Co. going only through the stamp layer (and only on the stamp); and the two-line "J&Co / +9.16.41" holes of the dated punch cancel going through both the stamp and the document tying the stamps nicely.

Hopefully the revenue collectors will chime-in if I have mis-stated anything here.