This question seems to come up a lot. It is purely a matter of personal preference. Some people charge an additional "daycare" rate, and others do not.
I will say that if you plan to start charging for the additional hours, this needs to be a decision that is made up front, at the beginning of the stay so owners do not feel taken advantage of when you suddenly ask to increase the price of the stay.
I do not charge an additional fee, but I am very strict about my drop-off hours. When I first started, I would be waiting on the couch in my pajamas at 10:30 at night, because an owner kept telling me they were "almost there" and "on their way" and "right around the corner". That was horrible, and I made some rules to keep that from ever happening again! Now, I simply let them know that they have to pick up their pup before 7:30. So far, everyone has been really good about it. I've even had some owners call to extend their stay once they realize there is no way they'll make it to me in time. This saves us all a lot of stress and worry. I don't even answer my messages after 7:30 lol As far as I am concerned, we are CLOSED!
Many commercial boarding facilities will charge an extra night once you pass the 24hr mark, so it is not un-heard-of to add this kind of fee.