Here's what I discovered:

You can break your model into many pieces then create blend targets for each piece then combine and merge the pieces back together and all will work as long as you create the blendshape nodes before you combine and merge the pieces back into a single piece of geometry. There is one problem though; a node is created that keeps track of the original vert order and the new vert order (once the pieces are combined back together) so that the blend targets can still affect their base geometry even though the base geometry verts will get reorders. The problem is that, depending on how many verts you have in your model, this calculation takes time. The blendshapes will not work in real time as you move the blendshape sliders.

Now, if you are only seperating one piece of the model to create blendtargets you won't have this problem since, when combining the two pieces back together, if you select the blendshape base geometry first and the rest of the model second then COMBINE the pieces, the blendshape base geometry will retain the order of its vertices and all non transform history can be deleted. This means that there is no need for maya to create a node to keep track of vert order changes since they didn't change in the part of the model that has a blendshape node attached.

I'm working on a practical demonstration now that will show a model deforming with the use of multiple blend targets that were created in Zbrush. I'll post the video clip as soon as I'm done...