Mongodb – Multiple databases through a single connection MongoDB, GridFS

Mongo will happily let you directly access any database on any individual node you hit. If that database is sharded, you can still access it but will only get results from that shard. This also means that you can have unsharded databases on a node and it'll return results from that unsharded database.

Yes, it is safe to directly access the replicaset members for that unsharded database.

It's also possible to do it through the MongoS process same as the sharded access. This may make code-paths easier, though it does add a bit of latency to the entire call.

• Database is a feature of Nodes.
• Sharding is a feature of Databases.
• Replica status is a feature of Databases.
• MongoS and Config servers represent the management layer needed to do Sharding.

A database that is not sharded does not need MongoS or Config, and can be directly accessed safely.

You feel like they should be separated because that makes perfect sense in the relational world.
But as you said in the NoSql world and in MongoDB in particular, you want to group like-items together. I've not done extensive research on Mongo, but have spent some time with the online classes and I believe the answer is to store them together. You probably realize there is no such thing as a join in Mongo and therefore if you wanted to get 100 rows and get their corresponding images, you'd have to get the IDs for the 100 rows and then get 100 rows by their identifier (object_id or whatever). In other words, you have to do manual joins.