The content of files are stored in the filesystem, by default in the alf_data/contentstore directory. The Lucene indexes are also stored in the filesystem, by default in the alf_data/lucene-indexes directory. The space hierarchy, categories and properties of the content are stored in the relational database (HSQLDB in your case).
The Alfresco database tables should not be accessed directly, since the schema does change from time to time (eg. between 2.1 and 2.2 there was some refactoring of the handling of qualified names that requires fairly significant changes to the database schema).
Another thing to note is that while HSQLDB is great for "kicking the tyres", it is not suitable for production use.
Cheers,
Peter