The first one. But it is a shortened way of saying "Did she do all right today?" so that may be confusing for non-native speakers. "She does all right today" is a statement, not a question.

Did she do all right today ? is the correct sentence and the one you should be using. Often, in movies and the likes, sentences are shortened in context because they can be understood. However, while learning English, it is recommended to use them in their full forms to avoid learning bad examples.