Does MongoDB track how many times each index is used in a query?
You can use $indexStats (new in version 3.2):
db.collection.aggregate([{ $indexStats: { } }])
Which, besides other information, returns the number of operations that used the index (ops property).
{ "name" : "_id_", "key" : { "_id" : 1 }, "host" : "test-dev:27017", "accesses" : { "ops" : NumberLong(2), "since" : ISODate("2016-04-21T14:15:57.846Z") } }