Yes, absolutely. YOU WLL LOSE ALL CUSTOMIZATIONS. Be sure that you do not want these customizations before you uninstall.
Well, because plugins are supposed to, and should be expected to clean up after themselves. If you disable and uninstall the plugin, as a developer, I am supposed to assume that you no longer want me to store all of that now useless data in your database.
Sure, if you are an Admin, just go to the plugin editor and wipe out the uninstall.php and then WordPress will not delete the meta data on uninstall.