You probably has multiple indexes, and the query optimizer is not able to select the one you want. What indexes are there you can find using the db.collection.getIndexes(). And, you can generate a Query Plan and see how indexes are being applied using the explain() method on the query.
In general, I think using of hint is not encouraged. Having more data doesn’t allow selection of a particular index, I think. How index is selected for a query depends upon: