HubKarma is your 'karma' or 'reward' that you get for back-linking other's good quality hubs that are related to your topic. You can do this by clicking on the 'suggest links' which generates related links (of other hubs) for you to add on your hub for maximum authenticity of your topic and good experience for the reader. So whenever a visitor reads your hub, and click on the 'link' you created, you're indirectly helping a fellow hubber to get some viewership through you which is reward in HubKarma points.
Eventually HubKarma points affect positively on your HubScore! The difference is not much but no harm doing it for long term scorings!
Hope that helps.