When you upgrade your version of WordPress, this should not effect any of your JobRoller files. Of course you should always complete a full backup before you proceed anyway, but in terms of JobRoller, you won't lose logo/settings/posts/job listings in the process of a
WP upgrade. Third Party plugins are not officially supported, and of course we can't guarantee that when you upgrade
WP that the plugin will continue to work.
The same applies for upgrading JobRoller also.. you won't lose logo/settings/posts/job listings, but if you have modified the theme files in any way (i.e. css changes, other code changes), then yes, these are generally overwritten. You have the option to download a patch upgrade if you prefer..so that only changed files are updated, or alternatively a child theme will help minimize the loss of customizations when upgrading.