Splunk does have issue where if mongod process did not shutdown correctly and try to start again, since Splunk does not try to kill off running mongod instance. You could manually kill them off and restart Splunk.
KV Store is not a necessary component to run Splunk, however, some app might use it to keep track of states.
Also to reiterate, the way to disable KV store is by editing server.conf:
[kvstore]
disabled = true
... View more