I used to duplicate the *.dll and configure one as a synth and the other as a tempo-based effect so I could use Nectar in whichever way I wished. Now with VST3 this isn't possible as Sonar only detects one version of the plugin. So how can I either configure Nectar for both usages of tempo-based effect as well as synth (so I can send midi notes to it) or how can I duplicate the *.vst3 in the folder and have Sonar X3 detect it?

Effects capable of receiving MIDI need "Enable MIDI Input" selected in the VST3 drop down in the VST header. Since X3, there should be no need to configure an effect as a synth.

I am not sure if I am understanding the OP correctly.
 
Nectar 2 (Production Studio) has three VST3 plug-ins listed separately (Nectar 2, Nectar 2 Breath Control, and Nectar 3 Pitch Editor (MIDI driven)). The Nectar 2 Pitch Editor can also be inserted as a ReWire device (Synth Rack->Insert ReWire Device->iZotope Nectar 2 Pitch Editor).

scook - as usual, a succinct very helpful and useful tidbit.

Thanks for making us aware of that!