Sometimes. It depends on the eatery. At Whispering Canyone and Prime Time, a milkshake is considered a beverage (but at Prime Time doesn't include refills).
At LC they were not included as a beverage but since the kid did not want a dessert, she said she would write it up as dessert and not charge for it.
I would imagine it varies as to what type of TS location it is.
My guess would be it is never part of the CS credit. I was even told by many that a large soda is not allowed on the DDP, although a few spots gave it to me anyway.
At 50's PT they are included, and even though you do not get refills... they bring you the remainder in the mixer cup and both times we were there (hubby and son got the PB&J shakes) that almost filled up a second cup for each. It is a big serving!