I recently released this APEX Plugin which enables you to add Badges/Counters to practically anywhere in APEX.

On release, two different people asked me the same question:

Can it be added to the Side Navigation Menu?

The answer is yes, and this is how you do it - although there is a native method.

Pretius APEX Badge Plugin Method

Create a Page 0 Dynamic Action like this:

Add an Execute JavaScript Code True Action

 /* 
  * Pre-render all tree nodes to the DOM without expanding them
  * This forces the TreeView to render the HTML for all nodes (including collapsed submenus)
  * while maintaining their current expanded/collapsed state.
  */
 $("#t_TreeNav").treeView("find", {
     depth: -1,  // Search through all levels
     findAll: true,
     match: function() {
         return true;  // Match all nodes
     }
 });

Create a Pretius APEX Badge [Plug-In] True Action, which must be after the one above, with the following settings:

 $(".t-Body-nav").find(".a-TreeView-label").filter(function() {
     return $(this).text() === "Employees";
 })

It should now look like this:
Add some CSS to Theme Roller. Choose either one of these:

Option 1: Make only Sub-menu Badges smaller
```
 /* Smaller Padding for Sub-Menus */
 .t-Body-nav .a-TreeView-label[aria-level]:not([aria-level="1"]) .notification-badge {
   padding: 0.1rem 0.25rem;
 }
```
Option 2: Make all Navigation Badges Smaller
```
 .t-Body-nav .a-TreeView-label .notification-badge {
   padding: 0.1rem 0.25rem;
 }
```
Still not looking good? Try playing around with the padding numbers (above) or Vertical Position attribute in the Plugin Attributes
Run the page:

Tip: If, for example, you add an Employee through a Modal/Drawer and Refresh the IR. Then the IR shows 15 Employees, but your Navigation Menu still says 14. You can refresh the Badge on Dialog Close using the JavaScript below.

apex.event.trigger(window,'theme42ready');

Native APEX Badge Method

Create hidden item on Page 0 named P0_DEPT_COUNT
Create a Shared Components > Application Computation like this:
Change the Navigation List Entry to a label like this - the square brackets are important here:
```
 Departments [&P0_DEPT_COUNT.]
```
Run the page:

Conclusion

Here are the two approaches side by side.

The Amber is the Plugin method and the Blue is the Native approach

There are Pros and Cons of each method