If both 32- and 64-bit plugin folders are used in the VST plugin path in Reaper's preferences, Reaper favors the plugin version which is listed last (if the 32- and 64-bit plugin versions have the same name)
Like it's the case, for instance, with the NI plugins (Guitar Rig, Kontakt, Reaktor, ...).
As example:
- 'c:\vst32; c:\vst64' favors the 64-bit plugin version (if the plugin name is the same)
- 'c:\vst64; c:\vst32' favors the 32-bit plugin version (if the plugin name is the same)
In general, it's a good strategy to keep 32- and 64-bit in separate folders. This makes it easier to distinguish between them (which is often not possible from looking just at the plugin naming alone). Or if you don't need any 32-bit plugins, it's possible to just add the 64-bit plugin folder to the VST plugin path (so only these are getting scanned/used - skipping any 32-bit plugins completely). The same applies the other way, as well: if you don't need any 64-bit plugins (you can just add/use the 32-bit plugin folder).
Many user (including me) are using separate (custom) folders for each plugin bit-version. Similar to the examples above.
Although many plugin manufacturers already allow choosing a custom install location, there are still some which install plugins to a default location regardless (at least under Windows). So to a certain degree it's unavoidable that some plugins (of the same bit-version) are spread across multiple folders.