CMS Databases are all built differently. Joomla, Drupal, custom applications and databases all use varying structures and data relationships based on the needs of the site. For example Joomla creates separate data tables for every component where as Drupal keeps all data in a single tables. Every platform has a different set of rules. Some are built on normalized structures, meaning master tables and relationship tables are built separately. Some use tables to generate IDs and some have it set up to be auto-generated. The database designer, the system analyst and the developer all have to use a very specific rule set in development.
Cloning a database means we would use the existing database and modify the code of the new site to accept data and rules. Ultimately this means we are drastically modifying the code of the Joomla system. However, this modification work essentially creates another custom CMS system from the Joomla framework, NOT a Joomla system. One of the great benefits of Joomla is that there are more than 5000 available modules. However, with a modified system would require customization to each module to fit the existing database structure. So you lose the convenience and stability of being on Joomla. (For example, all Joomla tables start with jom_, so the code is set-up to easily add on to the database, not so if the database is not a Joomla database.) Maintenance costs for a modified system would be much higher. AND very importantly, it will be difficult to utilize new developers because they would need to be newly educated on the custom set up of the system.
Cloning itself is far more simplistic in terms of replicating a database, however the big difference is in the modification work that needs to be done to the system.
The most beneficial option for 99% of the CMS world is to actually migrate the content from the existing database into a Joomla database. This requites mapping of the database and all the relational structures and rules and write a custom application to move the content into a new database. This is a safe and efficient means of migrating the data with integrity. Most importantly, this means that you have fully converted your system and can benefit from all that Joomla has to offer.