If you shard one collection from only one database, then you no longer have only one replica set... you presumably then have several (as many as there are shards).
So, yes, you should then route all of your operations through mongos(s). Technically, the results will be the same for unsharded collections and databases whether you query though mongos or directly against the replica set/shard ... but of course you would have to know which shard to query against, and that's the whole point of mongos and sharding - you don't need to know where things live.
Asya