It seems that there are two seperate type of cases being discussed that creates some confusion with the ops' original questions. He is, as I see it, talking about a case (some call it a holster) in which you insert your phone and remove it completely when receiving a call, getting or writing an email, etc.
I have one that is that way and have had NO issues with the S pen - or anything else - except that it is right where I want it to be when I need it, and is well protected from bumps, scrapes, drops and other problems, ad infinite um. So far, so good!