res: stored in a Java resource, such as a Jar and always read-only
File structure
.script contains all the statements to create the tables, alter them and insert the data. This file is created when you use hsqldb in memory. (so I'd say this is your database) Otherwise the database is stored in .data as other people already said
.lck is the lock file by which hsqldb knows whether the database is used/locked by a process. This file is automatically deleted when you stop the program.
.log is used to write the changes made to data. This file is removed at a normal SHUTDOWN. Otherwise (with abnormal shutdown) this file is used at the next startup to redo the changes.
.properties contains the properties with which hsqldb is initialized