MongoDB really sucks at count. It's a problem I've run into repeatedly with games that automatically submit highscores (ie without a name field/submit button) using an API call of ours that saves then returns the rank by checking how many scores are higher or lower than X.... on games that get millions of plays.

My solution ultimately ended up being to put the leaderboards that are doing that particular thing into a special "truncate" list that periodically deletes everything after their 50,000th score.