Try a manual scan and see if that finds them. You can also find out which plugins failed, and either manually select and point the Plugin manager to the folder they are in and rescan again.
Waves has recently moved things and locations around in Program Files when they updated restructured for their new V9 plugins and licensing for Windows 10 digital driver signing thingy's and contraptions. All Waves plugins both VST2 and the new VST3 versions are now all listed together in "Program Files" for x64 bit plugins and "Program Files (x86)" for x32 bit plugins.
So if your problems are with any Waves plugins you need to go and download the latest version of Waves Central, and get updates and reregister all Waves plugins.
Not as difficult as it sounds. Completely automatic if all Waves plugins have already been registered to one user name. Just select/choose to uninstall locally registered plugins and hit the "repair" button and Waves Central will do the rest.
But if you share Waves plugins with another registered user you will need the user's name and serial numbers handy or Waves Central will uninstall them, as it will with all keygen installations which can only be fixed with a credit card.

WHAT???? Waves wants $6000 for their Mercury Bundle??? How DARE they!