Other than what vitalker said, the other thing to be aware of is that some plugins can appear to be different when they aren't. What determines if they're duplicates is the NAME of the plugin (as shown in Reaper, which you can actually rename - hint: you can fix the problem by renaming "duplicates" to have identical names, if they really are duplicates).
For example... if you select first priority as VST3, and then search for Pro-Q 3 (Fab Filter Pro-Q 3), you will get both the VST2 and the VST3 version. The reason is because VST2 version is actually called "Fabfilter Pro-Q 3" whereas the VST3 version is "Pro-Q 3". These names are not identical, therefore Reaper doesn't think of them as duplicates.
Now, if I search up "CS-80" instead, I'll see just the VST3 version of Arturia's CS-80 V4 because the VST2 and VST3 version of this are both named identically as "CS-80 V4".
So, if you see duplicates listed still, check what is showing for the names. You can rename one of them to match the other's name identically, if you want, and that will then result in a duplicate disappearing.
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