1) Virtual DataPort database refers to a virtual schema comprised of data sources, views, base relations and stored procedures. When a Virtual DataPort (VDP) server is installed, a default database called "admin" is created, but you can create new different independent databases and add them different folders containing data sources, views and so on. Don't confuse these databases (virtual schemas) with the external databases you can access to in order to use them as data sources.
2) - 6) Denodo does not normally persist or replicate data from source systems to itself. It only stores metadata for the virtual views and integration logic and it gathers in real-time the data from the data sources. However, a cache can be used to reduce the impact of queries hitting the data sources and to speed up their executions. Denodo incorporates a cache module that stores local copies of the data retrieved from the data sources in a relational database. By default, this cache module will store the cached data in the Apache Derby database embedded in VDP and accessible through JDBC. This default configuration can be used for testing or for small data sets but it is not recommended for large data sets or on production environments. It is strongly recommended to use any of the external Database Management Systems available for the cache system (Go to VDP Admin Tool -> Administration -> Server Configuration -> Cache -> Database Adapter), especially in production environments. You can select a disk based or in-memory based relational database.
For further information about how to configure the cache, see Virtual DataPort Administration Guide (Section "Configuring the Cache"), that you can download from the support site (https://community.denodo.com/docs/view/document/Virtual%20DataPort/Denodo%205.5/Virtual%20DataPort%20Administration%20Guide).
7) The Amazon RDS Service allows creation of MySQL, Oracle, SQL Server, or PostgreSQL databases in the cloud. They are accessible via JDBC, so they can be used as a cache data store from Denodo. Performance has to be considered at this point, paying attention to the network latency between the Denodo server instances and the RDS instance.
Hope this helps.