The mongo docs specify that you can specify a query hint for count queries using the following syntax:
db.orders.find(
{ ord_dt: { $gt: new Date('01/01/2012') }, status: "D" }
).hint( { status: 1 } ).count()
Can you do this using the mongo template? I have a Query object and am calling the withHint method. I then call mongoTemplate.count(query); However, I'm pretty sure it's not using the hint, though I'm not positive.