A good farrier will use a packing under pads that contains some type of anti-fungal, such as copper sulfate or something similar. Not only is thrush possible under pads if there’s nothing between the pad and the sole, but leaving an empty space there shouldn’t be done anyway as it would allow all sorts of stuff, including rocks/gravel, between the pad and sole
But filling the gap can’t just be any ol’ material, it needs to have anti-bacterial/fungal properties