Have you looked in
Settings|Sounds & Notifications|Notifications tab. You can disable the "Display message on screen" option and only have it play a sound. If you can't find the "Low Battery Warning" under the events pull-down, then you will need to apply a tweak as suggested above. Instructions for the tweak were originally taken from Philippe Majerus' site but the link no longer works.
First get yourself a good registry editor such as PHM's free regEdit. Use it to navigate to HKCU\ControlPanel\Notifications.
Then look for a key named {A877D663-239C-47a7-9304-0D347F580408}. If it doesn't exist then create it.
Under that key create a new String Value named Default with its data set to "Low Battery Warning".
Exit out of the registry editor and go to Start|Settings|Personal tab|Sounds & Notifications|Notifications tab. Under the "Select an event" pull-down select the new "Low Battery Warning" event that you just created. You can then disable/enable both sounds and the message for this event.