I'm wondering what this floor is for? Living space, indoor/outdoor entertaining, existing or new building?
How fancy does it need to be?
How consistently will it be heated?
What are the chances that there will be wet conditions?
Laying tile (or hanging any thermal mass) over wooden joists does sound like a bit of potential trouble.
Wood and masonry move differently.
There's a chance that if the wood bows or sags, your tiles' edges might fall or wedge on one side of the wood, as well as the possible cracking you mentioned.
Filling the wood with sand/earth may make it more rot-prone, too. "Breathable" suggests you may be drying out any underfloor moisture (or spills) by evaporation through the floor.
I would want careful attention to proper drainage and
water exclusion before even attempting a floor of the proposed mixture of materials.
That's not even considering whether your
heaters (presumably electric?) would be affected by moisture.
Depending on the context, I'd be tempted to pick one dominant method, and stick with more typical/traditional detailing.
Either go masonry/patio style: skip the wood joists and just lay your heaters and flags directly on sand/fill;
OR go wood style: skip the flags and sand, raise the joists up a bit, and make it accessible through a crawl space below the floor.
You might also consider making the original wooden floor removable in sections - maybe something like 4x8 plywood sheets, but of floor boards or parquet.
The manufacturer of your floor heating units probably has some well-tested methods for using them.
If all their methods involve concrete, you might call or write and ask them why, and what alternatives they could see for a more natural and flexible setting.
If they have a method for heating under a wood floor, that might be closest to your original design ideas, and they could give you good advice about heat storage options and proper detailing.