Yep, it's not "obvious". My notes are here:
http://mayamel.tiddlyspot.com/#%5B%5BHow%20can%20I%20query%20what%20is%20highlighted%20in%20the%20Shape%20Editor%3F%5D%5D
I use pymel simply because it makes optionVars convenient.
Snip:
import pymel.core as pm
selData = [item for item in
pm.optionVar["blendShapeEditorTreeViewSelection"] if item][0].split("/")
bsIndices = []
for item in selData:
if not item:
continue
bsNode, index = item.split(".")
bsIndices.append((bsNode, int(index)))
print bsIndices
[(u'blendA', 0), (u'blendA', 1), (u'blendA', 2), (u'blendB', 0)]
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