Since I too have had this question/issue, I tried this.. it worked!
(nut using "-tcpShutdownForce", not "-shutdownForce" which Thomas gave
probably from memory). I never could figure out why it would stay
running, but with connection-pools, Thomas's explanation makes sense
(and -tcpShutdownForce seems to be required).

A simple Linux init script I use:

#!/bin/bash
#
# h2db
#
# chkconfig: - 80 20
# description: H2DB
# processname: h2db
# pidfile: /var/run/hsdb.pid
# config:  /var/tomcat/conf/

H2_HOME="/var/tomcat/h2db/h2-1.3.159.jar"
H2_DATA="/var/tomcat/h2db/"

# Source function library.
. /etc/init.d/functions

RETVAL=$?

start() {
            echo -n $"Starting H2DB"
            daemon --user www "java -Xmx256M -Dh2.queryCacheSize=0 -
Dh2.returnLobObjects=false -Dh2.objectCacheSize=50000 -
Dh2.pageSize=8192 -Dh2.maxMemoryRows=100000 -cp $H2_HOME
org.h2.tools.Server -tcpAllowOthers -tcpPort 9101 -baseDir $H2_DATA &"
            RETVAL=$?
            echo
            [ $RETVAL = 0 ] && touch /var/lock/subsys/h2db
}
stop() {
            echo -n $"Stopping H2DB"
            daemon --user www  "java -cp $H2_HOME org.h2.tools.Server -
tcpShutdownForce -tcpShutdown \"tcp://localhost:9101\" "
            RETVAL=$?
            echo
            [ $RETVAL = 0 ] && rm -f /var/lock/subsys/h2db
}

case "$1" in
 start)
        start
        ;;
 restart)
        stop
        start
        ;;
 stop)
        stop
        ;;
esac


exit $RETVAL

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