With our app, there's currently a list of notification icons in the left side of the page. This are to alert you to events or things to do (e.g. you haven't contacted customer x for 30 days, you have 3 orders to update).
View fullsize: http://i.stack.imgur.com/KXzND.png
The app is a pretty complex ERP system, so there's always a lot happening on the page. Normally I don't like hiding elements on the page, unless it's obvious why they're hidden. However, these empty notifications don't do anything (i.e. clicking on an inactive icon does nothing). I have two thoughts on how to progress.
Hide the icons
First, just hide the inactive icons. It will help remove some unnecessary elements, hopefully adding clarity / focus to the page.
View fullsize: http://i.stack.imgur.com/eWqkp.png
Have a blank slate for the icons
If there's nothing to notify the user, it would be an opportunity to provide a nice blank slate. For example, for the inactive order icons, it use the pop out menu to talk about how orders work and a link to create your first order. Obviously, this is really only useful for new users to the system. It won't have any benefit for expert users.