Ok, now I'm another step closer to understanding what happens under the stress.
HSQLDB files are located in data/hypersonic folder.
So this abnormal behavior occurrs when HSQLDB is cleaning localDB.log and moving stuff to localDB.script.new and then to localDB.script.
HSQLDB keeps all SQL statements there so that after abnormal JVM termination it will be able to restore the state.
If your stress is a temporary peak, you might want to increase the maximum size of localDB.log file from 200mb to several gigs and this way you're making HSQL transfer those SQL statements more seldom.
At least it works in my environment for my purpose...