As a native English speaker, I find sitting IN the cafe more likely to be used. If someone asks, "Where is the businessman?", you could say he is "at the cafe." You probably wouldn't know if he were sitting unless you had just seen him. In that case, you might say, " He is sitting at the cafe."
Firstly, I don't think you say about things that they сидит - they лежит or стоит somewhere but never сидить. (Not in Czech at least and I am fairly certain it is the same in Russian.)
And secondly, you don't use this about people. When someone стоит or сидит somewhere then he really sits, stands or whatever over there - you describe the actual state they are in and not just some metaphore of his beeing there.