Hi and welcome to Arturia forums.
I use Studio One 3 on Windows 10.
Studio One (S1) give VST3 priority over VST2 plugins, if they share the same ID like Arturias does. S1 will not show both versions then. To see the VST2 versions you either have to either stop VST3 support in S1 or prevent S1 from reading the plugins in other ways.
Are you sure, S1 read the path for the VST2 plugins you can't see after removing the VST3 versions?
S1 should not find plugins that's not there. Have you restarted S1?
Keep in mind that there is a name change for some plugins.
but once I try to use them (drag and drop or per menu) nothing happens.
If nothing happens, then it must be because the plugins is gone. Again have you restarted S1? And have you tried to rescan?
You say you have searched for duplicates, and found some. Don't you install plugins directly to the folder S1 use? I recommend to do that.
Also does that search mean, that you manually have looked in the folders that S1 read to see if the plugins are there and only one of them? If not, then i suggest you do that.
Perhaps also try to restart Windows.