Assuming that the subfloor boards are stiff enough to not give when you step on them, you can do as
@HotRodx10 suggests. My only concern is what is below the bathroom. If you fill in between the boards with thinset, where will it drop onto?
If you don't want to add 3/8" or thicker plywood, you can add diamond mesh to the subfloor and then screed the thin set into it and then put down more mortar with a notched trowel for the CBU. Use backer board screws as recommend.
Be sure to moisten the CBU and floorboards so that they don't draw out too much moisture from the mortar before it has a chance to set up.
The diamond mesh provides another layer of stiffness without too much height.
If you put down the plywood, use both screws and construction adhesive to get a mechanical and chemical bond.
Use Ditra or similar on top of the CBU or plywood to create an isolation membrane to prevent cracking. You can use Red Guard or similar product to achieve the same effect.
In my bathroom redo, I was going to put down plywood over CVT, but, I pulled up all of the tile. And then I put down the 3/8" CDX plywood. And then Ditra.
Just sayin..