Performance is something that we're always looking to improve and there are a ton of performance optimizations in JFBConnect. I'm honestly not sure off-hand why those two queries are duplicated. They shouldn't be. However, the jfbconnect_config table should have less than about 100 rows and those queries should execute in well under 1ms times. While we will look into why the query is happening twice, you won't see any change in speed after the 'extra' one is removed.
As for having both enabled, there should be minimal impact on performance overall. Having one more plugin enabled does add a little to Joomla's loading time as it has to instantiate the plugin, execute some code and keep it in memory during the page rendering. Our profile plugins do very little on every page load though and most of their heft only gets used during the login or registration process. During authentication, they will add anywhere from .2s-1s or so per plugin to interact with the social network, pull avatars, etc.
In general, if there's a plugin or module you're not using, disable it. It's good for performance and security.
I hope that helps explain,
Alex
Duplicated Query to #_jfbconnect_config detected in Joomla! debug
