Thanks for your help, I just have a couple of leftover questions to recap and confirm my understanding.
1) Because the Emote VST plugin controls the global state of the H9000 it doesn't really matter where you place it in your DAW session, on which track etc. The main advantage of using Emote as a VST plugin (as opposed to the standalone application) is the fact that the current state of the unit is saved as part of your DAW project, because the Emote VST plugin state is saved. Is that correct?
2) The advantage of using the External Effect option in Cubase is that you can set it up once, and then audio will always be routed the same way. However it sounds like what I am doing is functionally exactly (?) equivalent, except for the fact it involves more manual setup. Do you think that's the case?
You are correct that it doesn't matter where you put the Emote plug-in in your DAW, it will function the same wherever it is placed and only a single instance is needed. Another very useful feature of using Emote as a plug-in is being able to use automation in your DAW.
I'll have to refer you to my colleague for your Cubase specific question, but I believe you are correct in that it's just a different way of accomplishing the same thing.