You only need to scan the folders with the Waves Shell .DLL and .VST3 files.
64-bit VST3 file installs almost always default to: C:\Program Files\Common Files\VST3
I install all 64-bit VST2 files to: C:\Program Files\VSTPlugIns
You can almost always specify the VST2 install folder during installation. The only other folder I need to include in my scan list is the 64-bit Native Instruments VST2 folder. NI don't let you specify the install folder. Sigh.
C:\Program Files\Native Instruments\VSTPlugins 64 bit
Whenever I have a problem when adding new Waves plugins, I deleted the following folder and all of its contents. Waves rebuilds it the next time the shells are scanned.
C:\Users\Primary\AppData\Roaming\Waves Audio
Replace "Primary" in the URL above with your username.
The "Cache" subfolder is usually where the problem lies, but deleting the whole thing tends to solve a number of Waves plugin problems.
NOTE: You do NOT need to scan the Waves folder that holds the .BUNDLE files.