Does stopping the engines perform an implicit checkpoint whereby image snapshot

Using the stop-suite.bat|sh script creates check-pointed Appian Engine Database Files (kdb's). There is no need to run an additional checkpoint prior to running stop-suite.bat (to stop the Engines).

Great. That's what I wanted to hear. Thank you.

Yes.
Reference: forum.appian.com/.../Server_Administrator_Guide_-_Print_Version.html
"A proper shutdown of the engines automatically completes a checkpoint."

What happens where there are lingering engines that won't properly shutdown and you need to kill -9 them?

kill is not recommended. It may corrupt the KDBs and may end up with loss of data/process. I recommend creating the support ticket for help.

If it's dev and like notification engines or something that you don't mind loosing data then use kill.