Hi,
It's the template you're using which is still displaying the position of the module even though the module doesn't output any HTML.
Not much can be done in the module to avoid that.
The template should check whether the modules in a given position outputs HTML before displaying the position.
This page provides some code that can be used in the template index.php to check if the modules of a position return any content before displaying the position:
joomla.stackexchange.com/questions/4215/...-from-being-rendered
Advanced modules manager Pro offers the same feature to be able to hide empty modules, but apparently, it has the same issue with YooTheme templates:
yootheme.com/support/question/12981