I don't think it's a concern, first of all. Second, store owners will kick out non-paying customers as they have since time immemorial. You might as well ask how someone deals with pan handlers at the intersection on the way to their drive-through Starbucks. If the person is just sitting in a corner not bothering anyone, maybe someone will buy them a coffee, or maybe they'll be annoyed that it's too loud and leave, or perhaps they just look homeless but they're just mistaken for your run of the mill startup founder?
There are also lots of homeless people in other parts of the world. How do people in Paris or London deal with them? I don't understand why this exists an American-centric view here for such a general concern. Homelessness isn't unique to the United States, yet virtually every country on the planet has coffee shops you can walk into.