Let me clear up some of the confusion...
Firstly it's a NaN issue. These are basically float representations of what can't be represented, in other words, not-a-number. The thing about these is once you get one in a series of calculations, everything that comes after that is also a NaN. So yes, if a plugin does the wrong thing on a math operation, everything after that will likely first pop and then go silent. Things like square root of a negative number, 0/0, arcsin with values outside the range -1,1, etc.
Denormals are just really tiny numbers that are close to 0 but smaller than what a float can normally represent. Those do not cause a pop and do not cause silence. instead, they can cause unusually high cpu as the microcode could be assisting. Classic symptom was seeing high cpu with plugins when silence passed through them.
In terms of tracking NaNs down, yes you can bypass the fx bin on a bus or track and then further disable individual plugins to find the culprit. We had some historically in our plugins that were subsequently fixed, so be sure you have the most recent versions of the in box plugins.
As far as SONAR by itself causing NaNs? It's extremely unlikely.
Nor would we leave such a thing in our engine unsolved for years. We use SONAR as well.
Also, we regularly do checks for invalid float operations by unmasking exceptions and looking for issues.
If you are using non-commercial 3rd party plugins it's possible they aren't handling 64-bit very well.
Keith