I agree, waves has great support, they will give you detailed instructions from A to B

what i can say for sure - if completely remove Waves (checked files and folders being removed), rescan VSTs and so on
 
then Sonar hangs on all projects containing Waves plugins if i selected at least one Waves plugin to be loaded
(in save mode).
 
i believe this is Sonar problem, not Waves one.
 
i expect Sonar to provide "XXXX is missing, can't load" type of error message.
instead it tries to load plug in and goes to some kind of infinite loop.

Again, contact Waves support. Waves plug-ins are not handled in the standard way but via a shell. If there's any "residue" from the Waves plug-ins SONAR will think they still exist. They also need to be installed exactly the way Waves wants you to and there may also be issues with older versions co-existing with newer ones.
 
There are hundreds, if not thousands, of people using Waves plug-ins who frequent this forum. If it was a SONAR problem, you wouldn't be the only one having it. So if it's not a SONAR problem, attempting to fix it by doing things with SONAR will not help. I've had to contact Waves a couple times in the past and each time, the problem was solved in under 5 minutes. Both of them involved installation issues.

I will contact Waves for sure, just want to check if the behaviour can also be reproduced with plugins from other vendors (for instance I anyway want to replace Blue Cat vst2 plugins by vst3)

However I would like to underscore that
if Sonar reports there are no Waves plugins installed after rescan - then it is fully natural to expect that while trying to open project containing those plugins Sonar should NOT try to load them - as they are not among registered ones.

In other words it is expected that before loading project, allocating memory and so on Sonar first provides message about something missing.

Because currently it seems that part of the Sonar related to vst scan and part related to project opening do not sync with each other

biozel
However I would like to underscore that
if Sonar reports there are no Waves plugins installed after rescan - then it is fully natural to expect that while trying to open project containing those plugins Sonar should NOT try to load them - as they are not among registered ones.

In other words it is expected that before loading project, allocating memory and so on Sonar first provides message about something missing.

Because currently it seems that part of the Sonar related to vst scan and part related to project opening do not sync with each other

Then this sounds even more like an installation issue. Remember there are things like VST inventories stored in the registry. The behavior you expect would make sense for plug-ins that just put a DLL in a Vstplugins folder and leave it at that. As I understand it, the Waves plug-ins do not work that way.

So once you disconnected wifi, your Waves plugins failed to load.  I had this exact problem last month when working on my issues.  When I re enabled wifi Waves functioned properly.  I don't know why this happened, I was just glad it was fixed.  I ended up looking for all the Waveshell instances in my scannable VST folders and found several.  I removed most and kept one 9.3 in the 64 bit folder and the VST3 one.  I had 9.0 and 9.3 in the x86 folder, and one in the 9.0 in the 64 bit folder.  Simply moved those to unscannable folders.  Now Waves loads without hanging or asking for me to find the location of the Waveshell.
 
My suspicion is that for some reason the new Waves Central wants wifi enabled.  Don't know if that is true or not.

interesting thing: if Reset all VST settings in Preferences->File->VST Settings->Reset
then when trying to open some project when "Missing plugins" window occurs Sonar
also hangs so you can't even press OK on that dialog box

it seems that problem is solved:
 
* reset all vst plug ins in preferences
* remove and deactivate Waves including removing just all Waves files (search "waveshell" in Windows Explorer and just remove all containing folders
* restart
* install&activate Waves
* manual scan
* ???
* profit!

I had some issues today with a plugin. Softube drawmer S73. As soon as I removed it from the session, it went away.

 
I don't know if this helps but I was just about ready to smash my PC today. After 3 hours of struggle, while trying to mix tracks for work and dealing with horrible glitchiness on a machine that should never have such issues, and removing every plugin I could from my session in an elimination process (except 1...), I finally figured it out.

I had the Drawmer S73 on the mix buss. It was bypassed. I turned it back on and the machine stopped glitching. Bypassed it and the track stuttered like crazy. Removed it completely and it's fine. I emailed Softube about this today. Again, not sure if this is your issue but it could be as simple as that.

Good luck!