For some reason, I just don't think putting pebbles in the entire enclosure would be such a good idea.
Rocks is not absorbent so that won't help your smell. Pebbles are small and generally smooth so they shouldn't hurt your ducks feet but I imagine it wouldn't be too comfortable either since they will always have to walk on it (since entire enclosure is rocks). Once they poop on it, the poop will eventually get trapped in between the rocks, soon the rocks will probably clog and you'll have to try to rake it (which is probably difficult, rocks are heavy). I suppose you could try hosing it but that would just make it even more wet and the rocks act as a mulch slowing down the evaporation of water beneath it.
Placing rocks just for your swimming area or waterer to separate the mud from the water would be a better idea so they can't dig dirt and put it back into their water source.
Sand is pretty good (when it's dry) when you first start out, and you can scoop out like a cat litter. Once it starts to get wet, it is very smelly and messy. Since sand is pretty fine, it doesn't leave much room for evaporation of the surface beneath it. I'd think it would stay wet for quite a while unless you want to be turning it. Same with rocks, if you want to remove it because it didn't work so well, it will be a workout as it's pretty heavy to haul out.
As for straw, leaves, and hay, they don't absorb moisture very well unless you chop them up really well exposing more ends to absorb. From my experience, they mat down pretty easily with poop meaning you will have to put in labor to rake and turn it.
My best absorbent material has been dried pine wood shavings which I just sprinkle more on top as needed. Some brands are better than others. The ones we get here are very uniform, fluffy (will fluff back up), without odd sticks, wood chips, and odd pieces. I've used some brands that weren't as good so you will have experiment with the ones in your area. Shavings tend to work well when dry so if your enclosure is exposed and get lots of rain, this would not be your choice of material.