"But in some cases, some keywords will be more common than these words." => So if a word like "What" has 12449 references and you have a cooking site you're saying that the word "Spoon" might appear 16338 times. It makes sense.
Now, both words exceed the 10000 limit I mentioned in the answer. So they are both automatically ignored. Manually ignoring "Spoon" makes no sense and is redundant. It will only slow the searches unnecessarily. If you still consider this is relevant for you, you can always write a plugin to take care of it