As @PatJ commented, a ZIP file just contains files. Those files are extracted and placed in the proper folder, overwriting any existing files of the same name.
When a plugin is updated, the process gets the ZIP file from the WordPress repository, and installs it into a temporary folder. The update process then, after all files are successfully extracted, deletes the plugins current folder, and renames the updated (temp) folder to the plugin folder name.
That’s why an plugin update (not zip install) will delete any changes to existing files, or any added files that might be created. And why a plugin, if it needs to create files for it’s use, needs to place those files in the uploads folder (in a folder with the plugin name).
As for any updates to tables used by the plugin, that is the process that the plugin will start on the plugin activation or by reloading the admin pages (if the plugin has code that is run on admin pages). The plugin might show an admin notice after being upgraded alerting you to additional actions.
A zip re-install of a plugin will alert you that the plugin already exists, and will show a screen showing some basic information about the old and new versions, and ask if you want to replace the current version with the newer version.
Added
In response to the comment: a ‘regular’ update will result in the removal of all existing plugin files, replacing them with those in the update package. An ‘install via zip files’ will not fully replace plugin files; if a file has been added ‘externally’ (manually, for example), that file will still exist in a ‘zip’ update, but not in a ‘regular’ update (via the Admin, Update process).
The plugin programmer will have to add additional code that would do additional update tasks, such as updating a plugin table.