[db] handle broken repos without certificate

On versions before 1.18.0, adding a repo would add it as "empty" to the DB without a certificate right away and if there was an issue with it (e.g. typo in URL), it would stay in the DB until manually removed.
Our migration code did not consider such repos.
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Internal Server Error - Gitea: Git with a cup of tea
500 Internal Server Error

Gitea Version: 1.28.0+dev-477-g8b6ad49a5f