Is there any reason not to add a few tables to the WordPress database? I’m not too familiar with WordPress and wouldn’t want all that data to get flattened if WordPress was updated or anything like that.
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You can add tables to your database without any issue. WordPress will leave any custom tables untouched with updates.
I would ask yourself if the new table is really necessary. For example. If the new data really should just be a WordPress custom post type and stored in wp_posts. Or maybe stored in the meta tables.