Is there a process for starting and stopping CLM services when servers are rebooted?

I recommend to shutdown the apps within the normal server shutdown process.

If you are using Liberty it would be simple to add the server shutdown script, provided in the application/server folder to the correct shutdown level.
On Windows, you have the services with the start/stop scripts and this controls a proper shutdown of the app.

I'm using following apache deamon to register and start stop the service:

https://www.apache.org/dist/commons/daemon/

commons-daemon-1.0.15-bin-windows-signed

Here my registration script:

@echo on

rem Run as Administrator
rem
rem Liberty profile delivered with CLM V.6.0.1 has no built in mechanism to define the startup as a windows service. For this you need a helper tool. I suggest to create the service using Apache Commons Daemon to run CLM in Liberty
rem
rem    Download the binaries for Windows from http://www.apache.org/dist/commons/daemon/binaries/windows/
rem    commons-daemon-1.0.15-bin-windows-signed.zip
rem    Unzip the downloaded file
rem    Move the files int
rem
rem    C:\IBM\commons-daemon-1.0.15-bin-windows-signed
rem
rem    Create a script with below content and run it to create a Manual service. You need to change the values in the variables, and you might need to change other values too (e.g.  --Startup if you want this service to be automatic):
rem
set VERS=604
rem set APPLLISTTOREGISTER=RS DM RM QM CCM JTS LQE ALL
set APPLLISTTOREGISTER=JTS

set IBMPROG_FOLDER=D:\IBM
set DAEMONPROG_FOLDER=%IBMPROG_FOLDER%

for %%X in ( %APPLLISTTOREGISTER% ) do ( 
 set APPL=%%X

    call :SUB_SetServiceForAppl

)

goto end

rem ========= Subroutines ================
:SUB_SetServiceForAppl
rem Copy DB file to this server for restore
@echo .resister %APPL% %VERS% as windows service on this server
set DAEMON_EXEC="%DAEMONPROG_FOLDER%\commons-daemon-1.0.15-bin-windows-signed\amd64\prunsrv.exe"
set SERVER_VARIANT=Liberty
set SERVER_FOLDER=%IBMPROG_FOLDER%\Jazz%SERVER_VARIANT%%APPL%%VERS%\server
set SERVER_START_COMMAND="%SERVER_FOLDER%\server.startup.bat"
set SERVER_START_COMMAND_PATH="%SERVER_FOLDER%"
set SERVER_STOP_COMMAND="%SERVER_FOLDER%\server.shutdown.bat"
set SERVER_STOP_COMMAND_PATH="%SERVER_FOLDER%"
set LOG_PATH="%SERVER_FOLDER%\logs\daemon"
set SERVICE_NAME=IBM-BT-Jazz%SERVER_VARIANT%%APPL%%VERS%
set SERVICE_DISPLAY_NAME=%SERVICE_NAME%
set SERVICE_DESCRIPTION=%SERVICE_NAME%
set INSTALL_SERVICE_COMMAND=%DAEMON_EXEC% //IS//%SERVICE_NAME%  --Startup=manual --DisplayName=%SERVICE_DISPLAY_NAME% --Description=%SERVICE_DESCRIPTION% ++DependsOn=Tcpip --LogPath=%LOG_PATH% --StdOutput=auto --StdError=auto --StartMode=exe --StartPath=%SERVER_START_COMMAND_PATH% --StartImage=%SERVER_START_COMMAND% --StopMode=exe --StopPath=%SERVER_STOP_COMMAND_PATH% --StopImage=%SERVER_STOP_COMMAND%
@echo %INSTALL_SERVICE_COMMAND%
@echo %INSTALL_SERVICE_COMMAND% > %IBMPROG_FOLDER%\Register_%APPL%_%VERS%_as_service.log
%INSTALL_SERVICE_COMMAND%

@echo %errorlevel%
GOTO:EOF

:end