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Each email address which is entered has a high chance of still being used, and so those are the ones they focus on. By using a site like this, you could inadvertently be making yourself a target.
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This is exactly the first thing that popped into my mind when I knew about the existence of HIBP (a year ago):
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You may think I am being delusional but here is what I think:
They have a database containing more than 8.500.000.000 email addresses and hashed passwords. Obviously they can't heck them all knowing that most of them are throwaway emails.
By entering your email address there, you are telling them that you care about it and Hence there are high chances that it contains some valuable information.
Also, they provide a service to check if your password was leaked! If you enter your password then they can generate its hash and compare it with other hashes on their database.
I like the way you think : )