Can Drupal nodes and taxonmy be used to store "data" rather than "content"?
I recommend leaving the database structure to Drupal, its modules will handle all of the management process and you will not have to code anything.

Taxonomy is very flexible for creating categories.  These taxonomy vocabularies can be attached to a content type.  Create a new type and add fields for each applicable vocabulary.  You can make assigning values to each field mandatory if you want and Drupal will enforce the requirement when new content is generated.

You will then use views to filter through all of your content and deliver custom pages.  It is incredibly flexible but can take a while to learn.  Check out the "Taming the Beast" video series at NodeOne.SE for an excellent video series to master views.