The S-400 isn't even really capable of shooting down the basic "quadcopter" drones, they're too small and fly far too low. You'd have to be extraordinarily lucky to be able to hit one.
I'm talking about Ukrainian shahed-equivalents here.
9M96E/E2 can be used to shoot down shahed-like UAVs, but it's not something you'd generally want to do. They don't exist in sufficient numbers and are far better suited for shooting down missiles. It's something you'd do as a last resort, when necessary. Not something you'd do to shoot down thousands of drones.
This depends on the missile being used. 9M96E/E2 are the high-maneuvering ones used to shoot down UAV's which have ranges of upto 40/120 km. Multiple 9M96 missiles can be carried per launcher container, making them more far more compact with operational efficiency.
You are right that you wouldn't use this against a basic "quadcopter" drone as it is still too expensive, but Ukraine does indeed have far more sophisticated, speedy/evasive "strategic" drones. They are the undisputed world-leader in drone warfare. Many times the Russians have no choice.
All of the layered Russian air defenses shooting down Ukrainian drone swarms do mention the S-400, but unfortunately they don't give exact target count to each system, so it is difficult to correlate numbers.