I think it's an interesting idea. I haven't tried it, but would be worried about leaks over time. The bottles would need to withstand a fair amount of temperature cycling as they absorb and release heat. I suppose if you used beer bottles or similar that are designed to withstand internal pressure that might work.
thermal capacity of water is extraordinary however:
water: 4182
slate: 760
limestone: 909
brick: 840
(all J/kgdegC from
engineering toolbox) The larger the number the more heat energy a material stores per unit mass. So a smaller amount of water will store more heat energy, which could be an advantage in a suspended floor I suppose.