No, the reason the devices are shown as offline when you startup the Pi is as @NoneWhereTo described: battery powered devices only send out a heartbeat every so often (minutes/hours?, or when you press a button on the device), so when openHAB first starts it doesn’t know that the device is online until it receives the next heartbeat (which might be minutes/hours away).
permit_join shouldn’t affect this.
(As an aside, you can toggle between true and false for permit_join directly from openHAB if you’re interested)