It looks like Japan had major quakes in the '20's and '30's, but this was prior to modern elevated structures. There was an 8.3 in Hokkaido in 2003 and it caused major structural damage.[
en.wikipedia.org]
Bridges are not a fair comparison because they have massive anchorages at the ends. Are you going to pour mountains of concrete and steel every so often on your 40 miles of Peninsula HSR elevated like the SF end of the Bay Bridge?
All the media propaganda prior to the election depicted a depressed ROW, so basically we have a bait-and-switch. Furthermore I suggest that a ditch would be more secure than an elevated, which can still be attacked from buildings lining the route. The elevated's sound walls will be graffiti magnets. Extensive fencing will still be required to keep gang-bangers out. Ghetto and blight are the appropriate adjectives here.
If they are worried about security they should use the 101 corridor which affords a no mans land buffer.