The drivers have deprecated the count() function and added two new document count functions, countDocuments() and estimatedDocumentCount().
One option is to remove the count() function and then replace uses of count() with countDocuments(). I am not sure how we would communicate with users that we have deprecated this function, maybe through our regular documentation or printing a helpful error message?
Since we haven't really deleted code from the shell in such a way, we can also have count() call estimatedDocumentCount() and just update the behavior description.