Every update seems to just add a new shell but keeps the old ones,
thing is when I do a VST scan, PIM finds all the older shells and rescans the plug ins again so the scans take forever.
 
Can I just delete anything older than the latest version?

On my computer each "shell" contains different plugins and as a result I need them all to get all the various Waves plugins.  But the exact plugins in each shell seems kind of odd, I'm not 100% sure if what is in each one isn't personal to me.  I have 3 shells, 
 
WaveShell-VST3 9.7_x64.vst3 
WaveShell-VST3 9.91_x64.vst3
WaveShell2-VST3 9.91_x64.vst3
 
The 2nd 9.91 shell contains mainly plugins that have been updated recently or bought recently.  The first 9.91 shell contains the bulk of the plugins.  The 9.7 shell only contains Studio Rack (Stereo/Mono/Mono Stereo).
 
I get the impression that Waves is limiting the plugins in each of the two 9.91 shells based on count (perhaps some sort of limit?) and the exact plugins that end up in each shell may be a factor of what Wave plugins I have.
 

Noooooooooo.

Surely you can? I just the other day re-installed the Waves shell and my two free plugins (I got years ago) were still able to be restored.