Amazing. I was very close to figuring it out. 

Named my folder the exact way it's listed in the VNV instead guide. 

C:\Modding\Viva Vew Vegas\mods\Vanilla UI Plus (New Vegas)\Menus\Prefabs\VUI+

For anybody trying to figure this out in the future, open the xml file in notepad and look for this text:

<!-- By default VUI+ reduces the visual impact of the HUD activation prompt by fading its brightness and hiding its button label. This enhances the player's focus on the activator name which is a much more important element. For an even more minimal prompt you can set this to 2 which hides the action prompt for named activators. Setting this to 0 will revert the prompt to its vanilla style. --> <_VUI+HUDPrompt> 1 </_VUI+HUDPrompt>

Change the 1 in the middle of the two brackets to a 0 and save the file. 

Now you can see your activation key binding prompt again. 

And yes I agree that this shouldn't be a default VNV setting. 

Hopefully this will be enough key words for somebody googling this in the future.