The plans are really counting "allowed activations". So, for the plus plan that's 3000 "allowed activations". When you create a product key with, say, 1 "allowed activation" it increments the total used activations immediately. A customer can then activate and deactivate the key thousands of times if they want and it will still only count as 1 used activation.
When you delete a key the total used activations goes down by the number of allowed activations for that key.
Does that clear things up?