Does that span calculator used to decided maximum size of ceramic tile I can use?

You can use any size. The larger the tile size, the more important factor is how flat the floor is.
The span calculator only deals with wood subfloor structure. You use it to see if your existing structure is capable of supporting tile or stone that's within the minimum deflection criteria for either ceramic tile, porcelain tile or a natural stone installation.
You should have a minimum rating of L/360 for ceramic and porcelain and a minimum of L/720 for natural stone.

Currently I placed wonderboard and screwed it to the floor, but some screws are not totally into the board, they are a little higher than the surface of the wonderboard, is this ok? thanks

Those high screws can cause you problems with getting the tile to lay flat. Worst case scenario, you could have tile cracking when it's resting on a screw head.

What kind of screws did you use? Are they deck screws and do they have a phillips drive or a square drive, or something else?

The way I fix those stubborn screws is to drive one into the floor next to it and pull out the high one.

thanks, I tried, cannot make them totally flat with cement board, maybe 1-2 mm is ok? the screws I use is Buildex Rock-ON, phillips screw. it is said it is specially designed for cement backerboards.

Are you sure the rock-on screws you bought are for wood?
You really should try to get them at least flush to the surface.
Could be a problem if thinset coverage while setting is minimal.

Impact style screw guns work best for setting screws. A regular screw gun will usually strip the phillips heads before they are flush to the surface.

The normal trowel notch used for floor tile is 1/4 by 3/8 inch. this gives you a thinset thickness about the thickness of cardboard. any bumps bigger than 1/8 inch (2 mm.) will hit the bottom of the tile. get a counter sink drill bit and counter sink the protruding screws slightly. A quick fix is to give the protruding screw a good whack with a hammer and then sink another one about two inches away. This is a common problem with cement board screws, which is why I usually use epoxy coated deck screws.

tried to make the screws less than 1mm higher than the cement board. put tile on yesterday, looks ok now. how long should I wait before apply grout?

Is the same structure and same cement board good to apply marble?

16 to 24 hrs before grouting.
Input all the data into the span calculator but change the deflection criteria to L/720. If your existing joists span more than the allowed in the calculator report then you would not be able to install marble without reinforcing the floor structure.

I would use Schluter Ditra instead of the cement board if your floor meets their minimum requirements.

Stone installations should have joists that meet the span requirements with a minimum 3/4" plywood subfloor plus a 1/2" plywood underlay and an underlayment layer of cement board or a membrane like Schluter Ditra.

Deflection of single layer subfloor material between the joists is one of the big issues for a stone installation. Two layers of plywood at the correct thicknesses helps reduce this problem.