On a largeish collection, results from count() applied to a query appear to return the number of scanned objects instead of the number of objects returned by the find():

db.activity.findOne(

{'datacache.user.id': null}

)
null

> db.activity.find(

{'datacache.user.id': null}

)
(No result)

> db.activity.find(

{'datacache.user.id': null}

).count()
816

> db.activity.count(

{'datacache.user.id': null}

)
816

> db.activity.find(

{'datacache.user.id': null}

).explain()
{
"cursor" : "BtreeCursor datacache_user_id_1",
"nscanned" : 816,
"nscannedObjects" : 816,
"n" : 0,
"millis" : 44,
"nYields" : 0,
"nChunkSkips" : 0,
"isMultiKey" : true,
"indexOnly" : false,
"indexBounds" :

{ "datacache.user.id" : [ [ null, null ] ] }

}

Searching for values besides null in that collection is inconclusive: result count always matches scanned count in such cases, they only differ for null.