How can I smooth a seam between cement board?
You may break a few pieces(of marble) just picking them up.

A skim coat on either side of the joint will help.

Block feather with a concrete 'rubbing' block.

My marble floor always have Schluter Ditra under them.  I also use it with any questionable floor.

Ceramic tile can tolerate L/360 deflection, stone is twice as sensitive at L/720.

If you have any doubts about floor springiness, use an isolation membrane or stiffen joists or add a beam.  Cement board does little for stiffness.