So if it were possible to utterly remove the creature from existance, without any message, also removing it from time itself and the history of the world it wouldn't clutter your units list?
You probably removed hundreds of millions of them, but you don't remember.
Two tips for atom smasher:
1. Some creatures are too big to allow it to work (bridge won't close, like elephant calves), and some are even bigger (bridge will be destroyed while trying to smash them, like adult elephants). Creatures in cages are perfectly smashable though.
2. Surround your bridge with walls with one door, normally locked or tightly closed. Build a ramp or stairs and designate a 1x2 zone with pit and garbage disposal, on z-level+1. One tile must be over the hole (with bridge underneath) - this is a pit, and one tile must be over a floor, adjacent to the hole - this is a dump zone. Now you can pit useless animals (when small enough) and throw useless items to the same place. The door is to allow you to collect items/animals after change of mind, or if they were thrown there by accident. While mass dumping some dwarves may also fall into the pit, so it allows them to escape. The idea of a wall is to protect the wandering dwarves or pets while smashing.
Personally I also build a more complicated smasher - it works similar to the one described above, but dwarves throw items not on bridge, but on a mechanized hatch cover. The cover is over a magma cistern, with its own atom smasher. There are closed doors on diagonals on the hatch levels (diagonals - so miasma won't escape sideways), used to retrieve items. The atomsmasher in magma sea is used to dispose of magma-safe materials and grease which remains after burning larger corpses. Also there are doors to close the whole complex.