Sorry for confusion - I am a newbie to Raspberry Pi and Red Node.
With deploying I meant click on the Deploy button on the Red Node UI.
As far as I remember on my Windows installation of Red Node I only gave a value for credentialsSecret and httpNodeAuth in the settings file and the message was gone.
Where else should I give credentials? I don't understand the relation to MQTT here. Sorry.
That surprises me, it doesn't seem to throw any light on the current problem though.
At least you seem to have established that Node-red is not installed on a filesystem which has gone read-only.
The encrypted credentials file is used to store things like passwords and usernames for various nodes. It allows them to be kept secure and separate from your flows.
It looks like there is no file because you have not set up any nodes which use credentials.
Anyway, since there is now an empty flows_cred.json file I imagine that the warning will go away.
It's safe to ignore the other start-up warning about Projects too.