Item layers sound easy in theory, but they aren’t trivial to implement.
For example, currently items in rubble are always buried in it. This is a bug (zombies killed over rubble get buried there), but it’s minor enough that no one took the time to fix it (because fixing it would probably take quite a bit of time).
Burial could be handled by making some sort of a grave terrain within which the body would be sealed.
But implementing burial would probably be a temporary measure, because as far as I know we will eventually have dead NPCs raising as zombies. So if you want to “pay respects”, make a funeral pyre instead.
If you want to remove trash, first try to burn it (most non-metal, non-rock stuff will burn in raging fire), then drive over the rest with a car.
Z-levels will probably solve it, but z-levels look quite far from here. DDA isn’t all that new, there are cash bounties on Z-levels and yet no one implemented them yet.