Of course for this instance, your control would be a room full of mugs, and your test would be an empty room of recently atom-smashed mugs. Then again, you'd also need a control of no mugs to start with...
Control is just pulling the lever without building or smashing any mugs.
Because building and destroying mugs repeatedly did not lead to lag, then there must be a properly working clean-up function. The test of the atom smasher is to see if this clean-up function works in all situations.
For example, Peterix was talking about how you can use DF Hack to eliminate many objects, but that because it is a memory hacking tool, it doesn't actually always trigger all the proper routines, and can lead to undesirable behavior, such as eliminating magma, but not actually changing the temperature of the tile back down to non-magma temperatures, so it still melts anything in the tile.
Likewise, magma-casting, ice-forming, or other "put a wall over it" destructions of items can lead to very strange behaviors, especially when you carve them back out.
Further, there are reports of events like magma dumped objects not properly being cleaned up.
By testing each of these different cases in isolation, I can try to zero in on what specific problems there might be in the cleanup routines, and file bug reports for them.