Hola Dave

In this context yes, we use the word ventanilla to refer to the window/pane/counter that you find in the bank for example or any institution where you need to present documents. If there is no physical window/glass and it's only a desk with a person, we may still call it "ventanilla" as a default, however you may find that we call them "mesas" as well, so you may hear something like: "Pase por la mesa número 2 cuando llegue su turno." (Go to table/desk 2 when it's your turn.)

But in any case we are always referring to the "spot" (whichever physical appearance this may have) where a person is going to help you out with your documents, transactions, questions, etc. 

Saludos