Which one of these is correct?
She would have destroyed them if she wanted to
She would destroy them if she wanted to
To my knowledge the first one implies a hypothetical situation about something that has already ended am I right?
You are correct in that the first sentence deals with a situation that ended in the past.
The second sentence sounds more like she does have, and has had, the power to destroy them, and presumably still does.
EDIT: "She would destroy them if she wanted to" - I'm going to change my opinion here. This doesn't really say anything about the past, only what she would do if she wanted.
Both sentences are correct, but they mean different things.
If the above are questions, say in an examination, the answer to score should be: She would have destroyed them if she had wanted (to). She would destroy them if she wanted (to).
In other situations, we can have assumptions and the answers might also be different.