This is security
Well, I guess for the backend you can make the modifications - at the end you trust your backend users right?
So, go to
components/com_hotspots/controllers/hotspots.php find this code (at around line 127)
$filter = new JFilterInput(array(),array(),1,1,1);
$row->description = $filter->clean( $description );
$row->description_small = $filter->clean( $descriptionSmall );
change it to
$row->description = $description ;
$row->description_small = $descriptionSmall ;
Now when you disable the editor for the hotspots, the script tag should also be saved in the database....
But don't put any javascript in the short description, you risk to brake the loading of the hotspots on the map...
Let me know if this helps!
Daniel