Is it possible to use something like \'exists\' in a Mongo query to return this record based on an ID?
Something like select where \'ids\' contains key \'123456\'
As you're searching for the existence of a field with a given name, $exists is the operator you need (see Advanced Queries).
e.g. something like:
db.YourCollection.find({ "ids.123456" : {$exists: true}});