Since the last release all my plugins have been duplicated. 
 
I think there's a reason because the icon looks subtly different - does anyone know for certain?

VST2 vs VST3.

bapu is correct. look at the little icons next to the plug ins. they indicate 32 / or 64 bit plug ins.
go to VST settings and check the box "hide all related 32 bit plug ins".
this way you'll only see the 64 bit plug ins of your duplicates.

If you view the plug-ins in the Browser, and the Browser is docked, there is an info line at the bottom that gives info about the selected plug.  IMX, VST3 is always above the VST2 version in the list.

That makes sense, but interestingly "hide all related 32bit plug-ins" was already ticked. Hmm.

VST2 vs VST3 is different from x32 vs x64

I've found the difference.
 
Both plugins are 64bit - but one is VST3 and the duplicate is VST2 (just as an early post mentioned).
 

 
The tick box in VST settings is "Hide Related VST2 Plug-ins" (not 32bit).

 
Does this mean that this feature isn't working correctly?

It means iZotope does not support the option. It is up to the plug-in manufacturer to add support for VST3 migration. 

OK, can someone shed a little more light on this feature?
 
Sonar's user interface is displaying two plugin's with the same name except one is VST2 and one is VST3.
 
That implies to me that Sonar has all the information it needs to hide the duplicate - unless there's more to it that I don't know.

Something to consider.  I don't use the Hide VST2 option because some vendors have great VST3 versions and some don't.  For example, I ALWAYS want Waves VST3s, but I NEVER want an IKM VST3.
 
So I use the Plug-in Manager exclude function to hide IKM VST3s.  You can also use the Browser categorization feature to go thru and move VST2 plugs to a different category so that intention is required to choose a VST2 over a VST3.
 
It's kind of a pain and I don't know why "Hide VST2 ..." isn't.  I'm only suggesting that you may not necessarily want that global option anyway.
 
Even easier is to just remember the order is always VST3 then VST2 in the lists.  This doesn't make the list any shorter, but it doesn't require extra work to get what you want.