The ID is just an identifier in the database. Every new row (site) is added at the bottom, so you will always get a new ID. This is how MySQL works. The only way around that would be a manual edit of the database.
I wouldn’t worry about that. The ID doesn’t matter on the frontend, and reusing old IDs could lead to conflicts in other part of the code (plugins, users, other tables) that were using the old ID to change their behavior.
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