1. Help me, please?

2. Will you help me, please?

3. Help me, please.
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Does #1 mean #2? Because of the question mark, #1 is different from #3, right?

1 and 2 mean the same thing, yes.

3 is more of a statement or command than a question. You'd be able to tell the difference by the way someone said the words. A question would be indicated if the person's voice went up at the end. A statement would not.