Given only what you have provided, after all is unnecessary:
If you're new to the school too, don't be shy and talk to people! Maybe they're not so different from you?
Adding after all implies an assumption or expectation is, or may possibly be false. If the previous sentences established an assumption or expectation then it makes sense to include after all. Otherwise after all works best when the assumption is provided inline.
An example of a possibly false assumption is people who speak or dress differently will not have much in common with the listener. This could be phrased as follows:
If you're new to the school too, don't be shy and talk to people! They may dress or speak differently from you, but maybe they're not so different after all?
Sidenote: The sentence structure provided is slightly unusual. The intent would be understood by a native speaker. However, taken literally, the structure implies the listener is being advised to avoid the act of talking to people when being shy.
Consider revising to:
If you're new to the school too, don't be shy. Talk to people! Maybe they're not so different from you after all?