The two can have different meanings in my part of America (Western Massachusetts). For instance, "She is at school." means that she is actually in the building attending a class at the time the speaker made the comment. If you ask someone if they are in school though (especially someone who is between the ages of 18 and 25), you are asking them if they are taking classes at a college or university. Some people don't go to college because they don't have money to go, so this is how you would ask them in natural American English: "Are you in school or are you working?" "In school" also be used like this: "The things we have to learn in school are so difficult." Here it means the things you learn in a classroom while attending a college or going to a particular grade, middle, or high school are difficult. For instance, some people find calculus extremely hard. You could rewrite this sentence as "The things we have to learn in a classroom while attending a college are so difficult.", but it sounds less natural even though it is grammatically correct. Plus now it only mentions colleges instead of making a statement about all schools in general. :)

No difference to me. At school more Br Eng, in school more American.