We were told to leave these gaps between the sheets. Can we use silicone caulking in these seams or should we use thin-set and tape?

Use the correct modified thinset for the tiles you will be using and the correct fiberglass tape for hardi backer boards.
I tape and thinset the seams when I get to them while tiling to avoid any lumps or bumps in the seams. Be sure to mist or sponge the cement board with water as to not dry out the thinset prematurely. Use silicone caulk for the corners and the edges after the tile has set. I usually grout after the silicone has cured so as not to get grout in those joints that expand.