What should I do about excess flex in cement board that will be behind tile?
Since they're up, I agree adding blocking is a PITA.  

However, if its an inside wall that you have access to the other side of, use a "BIG GAP" polyurethane foam.  Drill a series of 1/4" holes every 12" down the middle of each joist bay.  Spray a 3 sec burst in each.  Wait 12 hr and try the flex, it should be quite firm now.

You may not want to do this near the plumbing valve, for replacement purposes.  It won't hurt it, though.