How to store/manage/display data sets in Drupal without using the node/entity systems?
Have a look at the Forena module which can be used to display (= query, not update) data stored in databases external to Drupal. It comes with a full suite of Supported database connections ... such as MySQL, MS SQL, Oracle, Postgres or any PDO compliant variation.

For more details about Forena, 2 types of documentation are available:


Community documentation.
Documentation that comes with Forena, which you can access right after install and enable of the module. Checkout the demo site for an online example of the Forena Documentation.


The Sample reports and graphs are fully functional, such as the drill downs available on the Master Summary with drill down. To filter data (by the users), you'd typically use "report parameters", which you can see in the sample report "Users in cities". On top of that, using Forena "skins", you can also use the amazing "dataTables" (and its widgets, such as sorting by selected columns).

It also includes a UI for either creating your reports (the WYSIWYG Report Editor) and/or for creating your SQL queries (the WYSIWYG Query Builder).

Disclosure: I'm a co-maintainer of Forena.