Warning "Encrypted credentials not found"

ls after reboot:

admin@raspberrypi:~ $ ls -l ~/.node-red/*.json
-rw-r--r-- 1 admin admin     0 Jul 19 21:09 /home/admin/.node-red/flows_cred.json
-rw-r--r-- 1 admin admin  1144 Jul 19 21:06 /home/admin/.node-red/flows.json
-rw-r--r-- 1 admin admin   448 Jul 17 18:49 /home/admin/.node-red/package.json
-rw-r--r-- 1 admin admin 22560 Jul 17 18:49 /home/admin/.node-red/package-lock.json

Deploying what?

Did you actually set a credential value (e.g. username and password in an MQTT node) and deploy.

There are no credentials if you don't deploy any!

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.

You need to add a node that uses credentials, such as an MQTT node. If you don't have any nodes that use credentials then possibly the file will not get created.

Where is no relation. Just that you set one type of credential and deploy. That will generate the creds file.

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.

That means that the service has not been enabled to autorun on boot. A better command to run to check the user might be
grep User= /lib/systemd/system/nodered.service