I have a very few large stones on the bottom of my pond. They are there because they serve a purpose.
Pumps, and whatnot sit on them, so they are not directly on the bottom. And there is a couple of cement blocks, which serve as dual purpose, "hidy holes" for the fish, and keep things off the bottom as well.
I cleaned out my header pond last week. pumped it dry, and got all the sediment out. The stream bed is full of pea gravel, and should have been cleaned out at that time, but time didn't allow it. I did manage to hose it down, thus removing a bunch of sediment, but it's far from being "clean". Now I've gotta get to the big pond. I'll find a way to vacuum it like one would do a swimming pool.