I recall reading that the pylons had vertical and horizontal dampers to protect against earthquakes (among other minor natural changes), so wouldn't those dampers be able to cancel out the shear waves?
No. Well, I suppose you could design an active vibration system to (almost) completely cancel the vertical vibration motion, but know you're talking about a powered system in each pylon of incredible complexity.
Passive resilient systems could help with higher frequency vibration (above say 100 Hz or so, depending on the forces and weights involved), but for lower frequency vibration (especially below 20 Hz), the resilient elements would have to be so compliant that even a gentle breeze would create very high vibrations in the guideway itself, which would be incompatible with the speeds of the cars inside.
You could make the pylons so massive that the forces from the vehicles couldn't move it, but again you're talking about higher construction and material costs, as well as visual impacts.
Vibration from trains is proportional to the unsprung weight of the vehicle (basically the axle, wheels and traction motors) rather than the vibration of the whole vehicle (which is isolated by the primary and secondary train suspensions). For a heavy rail transit vehicle (NYC transit, MBTA Red Line, CTA vehicle, etc), you're talking about 2,700 kg. I don't have numbers handy for HSR trainsets.
The plan uses an air bearing partly because an air bearing is exceptionally stiff. It's not like a hovercraft, with all that ability to squoosh up and down. So the unsprung weight might be the weight of the entire vehicle.
edit: though, mind you, the whole capsule also has mechanical suspension