In practice, the MongoDB Field Storage module will be used in a situation with a lot of fields/data.
There are some remarks to use this sub module.
Problems with Views
The contrib module Views will create standard queries suitable for relational databases. There are some solutions for this:
Solution 1: Search with facets (Search API/Solr)
MongoDB is chosen for a large number of nodes/fields. In such a situation the Solr technology (Search API) is often chosen. This technology will index the nodes with the chosen fields, in order to search the data faster. Views can make use of the data indexed by Solr.
Solution 2: Not all content types 'convert' to MongoDB
As we told before, a choice can always be made not to 'convert' certain fields/content types to MongoDB, but to still use the default storage_type/storage_module as storage (field_sql_storage).
Solution 3: Using EFQ Views
Contribution module EFQ Views will use EntityFieldQuery as query back-end.
Paragraphs/Field Collections
Since MongoDB is not yet widely used (about five hundred Drupal websites), there are still some bugs in this module.
Calibrate is maintainer of the MongoDB contrib module and we have made sure that MongoDB will work with Paragraphs and Field Collections.
Directly addressing MySQL database (db_query)
There is always a chance that certain (contrib) modules will directly use a MySQL query by means of db_query. A golden tip is to always test all new functionalities when using new contrib modules. This way, any problems can be solved faster.
If you choose to use MongoDB, it is best to install and configure it at the start of your project, so that people can notice the above problems faster.