Firstly: Using a Windows machine – would I need to select the H9000 as my audio interface to make use of the 16 x channels over USB? Or, will it run in parralell to my Antelope Goliath? 

I think you can only have one USB audio interface active at a time on Windows, but I will check with my colleagues.   An alternative would be to use a MADI expansion card in the H9000, which will give you 32 channels of IO between the Goliath and the H9000.  We haven't tested this configuration as we would need to acquire a Goliath, but assuming the routing supports it, that should work.

Secondly: I work with 3rd order Ambisonics which means 16 channels audio channels per track. Could I insert the H9000R on one of thise tracks and apply the same instance of a reverb preset to each of the 16 channles?

Yes, you should be able to have 16 instances of the algorithm running and set up parallel routing so that they are all independent.