Presumably they do. Sure there are arguments against it, but on the pro side: if people are going to spend a day on their laptop, do you want them buying your drinks every X minutes/hours, or do you want them elsewhere?
So they actually don't mind if you come in and order the cheapest cup of coffee they have, camp on a table all day, and keep coming back to the counter for free refills. They just care that you do it often, and that you minimize their credit card fees when you do it.
Of course, if they know you enough, they'll eventually figure it out by looking at your face.
Only store I had a problem was in Nacogdoches, TX -- somehow, they didn't allow refills -- citing some health law disallowing it , so I guess it can vary by store.
The one store I was treated differently (which was a direct operation store) was little surprising to me, but might have been something to do with bizarre laws in their local jurisdiction, in which case they wouldn't have much choice.
It could have been better if they could accommodate me somehow, though...
Also, to your specific point - when people choose restaurants they often go where there's a crowd (the food must be good here), not to an empty restaurant. The situation is a little different because Starbucks is so pervasive, but don't discount the customer draw of a bustling store full of people.
Over the years just kind of casually observing the placement and layout of the stores, it seems that they are maximized to be easy to access by the morning rush crowds as well as the lunch and after work rushes. Also, a pronounced increase in drive-through locations.
I could imagine that the majority of a location's revenue comes from walk-in/out business during peak times, and the tables could stay full with little rotation all day without appreciable impact on revenue, while solidifying the chain as a go-to "third place", especially for the business class.
Any former employees here to chime in?