During a WP ‘core’ update that happens to modify the database, I believe that there is no ‘overwrite’ of tables or removing tables in the database.
If you add a new table to the database, that table will ‘survive’ the next WP core upgrade.
You’ll only lose data if you reinstall from scratch, and specify another WP table name. But there would be few reasons to do that.
A plugin or theme will make some changes to the tables. A plugin might have options that are stored in a table. And their upgrade might add/modify one of their own tables, but not the WP-based ones.
Updates are good to do, IMHO. I check for core/themes/plugin updates daily, and install daily when needed.
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