Just curious to know that will I have to deactivate all third party Wordpress plugins before I upgrade (automatically) to the latest Wordpress AND JobRoller versions?
It is recommended that you do so. Ideally you would, because there are no guarantees that third party plugins will work with the latest version of WordPress or JobRoller (we don't officially support third party plugins anyway). But it's often best to test that everything is working as it should before you activate plugins..