I don't think this is an issue. As I noted, forms are generated from time to time, but, like yours, are full of zeros and don't get filed.
When you file, choose the option to see only those forms that are required for filing, and see if the 8889s are still there.
And even if they are for some odd reason filed, an 8889 full of zeros will have no impact on your return. You can prove this by deleting the forms now and seeing if your refund or tax due changes.
To delete a form in the Online product, go to Tax Tools on the left (when you return is open), then click on Tools underneath, then in the center, click on Delete a Form.
To delete a form in the desktop product, go into Forms mode (upper right), select the form on the left, then click on Delete at the button of the form screen.
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