I upgraded from Kontakt 5.4 to 5.6. The standalone contact is now 5.6 but the version within Sonar is the old one. Any hints?

it may well be that you installed 5.6 parallel to 5.4 due to changed installation paths ...
 
check the paths where K5 got installed to (this may have changed in case you moved to NI Native Access), also check where your VST paths in Sonar are pointing to (be aware that installing Sonar 2016.11 messed with the VST path, which is not good IMHO)

I had the same problem - standalone updated, but DAW version did not.
I solved it by going back and forth between their 2 upgrade programs (Native Access and Control Center?) till finally their older program (Control Center) saw that it had not upgraded properly.  
Actually had this happen twice in a row... they have had 2 recent Kontakt upgrades.  Hope this helps you.

What I don't get is why there's 3 Kontakt 5 listings in the Insert Softsynth menu with no way to tell them apart without going into Plug-in Manager, double clicking each one and renaming them.  Same goes for every other plugin with multiple versions. Sometimes renaming them doesn't work either.  Maybe it's time to update the Plug-in Manager.

It's not the plugin manager's fault. It's just reporting the names that the plugins themselves return to it when it queries them during a scan. Fortunately, we are able to rename them ourselves, which is handy not only for Kontakt but all plugin families that start with the same word, e.g. FabFilter stuff.
 
The difficulty the OP was experiencing was that the NI installer was writing the updated DLLs to a location different from what he'd been using previously, resulting in duplicates.
 
The first time I noticed a version difference between SONAR projects and standalone Kontakt and realized why, I copied the newer versions into my preferred location. The problem with that solution is that I'll have to remember to do that each time I update Kontakt. With some other plugins (e.g. Melda) I just gave up trying to impose my will on them and let the installers stick 'em wherever they want. That's also an option for Kontakt: delete the old DLLs and add NI's preferred location to the scan folders list.

You can actually tell the 3 versions of Kontakt apart.  If you select one in the Plugin Inspector/Browser window down at the bottom is a status bar that tells you about the selected instrument.  Each of the 3 Kontakt instruments has a different number of outputs.  You can then (inside SONAR) rename them (it's a new feature that was added a few months ago).  You only need to do this once now (unlike before where SONAR wouldn't keep name changes after updates).
 

Cool. I had to rename them each time Sonar did a scan.

I think if you do the rename in the Plugin Manager it won't keep them.  You have to do the rename inside SONAR.  It now saves that name change to a local database and does keep/reapply the name changes after rescanning. You have to be running recent versions of SONAR too. It is one of the very nice improvements. 
 
You can see in the screen shot I've renamed the 3 versions of Kontakt with the number of outputs and it has kept them through a number of VST rescans and new releases of Kontakt.
 

beware , this vesrions is way less solide that old one when it comes to perf specially voices .... be sure to compare , keep both veresions and compares heavy patches ...confirm even during a discussion i had with Spitfire guyz ...

You can change the initialization file to display both the vst name and the dll name from the "Insert Soft Synth" menu.
 
Example display after changing value to 2:
 
Kontakt 5
Kontakt 5  (Kontakt 5 16 out)
Kontakt 5  (Kontakt 5   8 out)
 
 
To change the initialization file:  fill in the "option" and "value" boxes as shown below and click "set".
 
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