The main problem I see is, the weapon seems to be one-shot. All the kittens would fall down, meaning it would have a fairly long reload period.
I think you missed the "large room completely filled with kittens" part. only one tile has a hatch, and as kittens wander, they will fall when they end up on that tile, not all at once.
Wrong, creatures that cannot fly will not path to a tile that cannot be walked on, any tile that can be walked on cannot be fallen into (except from above, of course) and thus only a kitten that is already on the drop zone will be dropped down the tube and into the kitten-hammer-rifle. The room must be either 1 tile total, 1 tile wide above a row of kitten-hammer-rifles(resulting in massive lag as the hundreds (you need them) of kittens and cats would be able to path to other tiles.) or you may build several separate pits above individual kitten-hammer-rifles (probably the most effective without going nuts with the lag)
The accuracy isn't going to increase no matter how the hall/machine is designed, but in a 11x11 room with KHRs loaded with >30 felines each on every other tile (or every tile as far as the traps go, but the kittens are best kept in 1x1 cells for lag reduction), when activated when an enemy squad is in the middle (you'd want to pull the lever/activate it when they're just outside it) will result in massive casualties (probably 80+% of invaders wounded if not dead) as blood-covered balls of pure adorable fly everywhere, resulting in instant and simultaneous cat-astrophe and the retreat of any survivors, or at least of those that are capable of going anywhere. A hall including several of these rooms will likely result in total annihilation of any seige
God I love parenthesis, NEVER leave a detail un-detailed.
Although, I guarantee this sort of thing will result in a tantrum spiral unless you've designed some ingenious(ly-simple) mechanism to deliver the animals directly from holding cages to the pits, or you're dwarves are incredibly awesome/used to tragedy, as nearly every feline left alive and outside a cage will adopt/be adopted within a dwarven fortnight (2 weeks)