Ardour does not see three inputs of, say, a LADSPA Vocoder. It sees only two. LADSPA Vocoder has three and you need three to create an effect.

Ah, ok, now I guess I understood: one of the inputs is MIDI...
But you can do the same using just audio signal inputs in the vocoder, and a simple synth with its output connected to one of the vocoder inputs. Right?