Normally the server will remove the application from HA-JNDI view if you shutdown.
It should work if you do not use UserTransactions.
Removing HA-JNDI is not a good idea in a clusterd environment.
What kind of errors do you see?
my error is not directly with HA-JNDI, and finally i found my application has internal logic error about this service, so i have not continue to check how to shutdown HA-JNDI under a cluster environment. and as you said, it is not a good and reasonable idea.