Is it seven o’clock (yet)?

The difference is that #3 doesn't give any indication of whether the speaker is surprised or not. In context, it would probably be easier to tell what they mean. As a standalone question, it's just that - a simple question.
 
Is it seven o'clock yet?

It's probable that something is supposed to happen at seven o'clock, and the speaker is feeling impatient.
 
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