How to avoid the VST DLLs multiplication in a new install

Hello, 

I am setting a brand new DAW with VST and utilities I gathered along the years. Lot of time... 
First, I installed almost all my stuff while specifying the folders to drop the dll's, in an attempt to avoid dispersion of the said DLL's and keep the things organized in the windows directory. My former DAW had become a mess over the years and I wanted to keep everything straight and simple. SPlaT sees everything but there are double instances of some plugins appearing here and there. Obviously, I checked the "replace VST2 (32bits) by VST3" option on the preference menu. So, to my surprise I actually see many plugins duplicated here and there in various folders. The only reason I can see is that I updated them as soon as installed... but the same thing goes for my Waves stuff which was installed once, already up to date. 

I have no idea as to why I have so much dll's duplicated. In fact, Sonar PLT plugins scan amounts to over 1300 and there are some more to be installed... I understand it is a minor issue that I can resolve manually but I really wanted one set of dll's for the 64 bits side of Win10, and one set for the 32 bits one, along with the unavoidable VST3 folder. I am conscious that moving some VSTs in a unique folder may induce problems in their updating process, when required. 

Any expertise to share?

Thanks in advance for your time.