I copied a flows.json from one node to another node (new installation), there are no credentials used in the flow, NR starts up:
9 Nov 16:31:12 - [warn] Encrypted credentials not found
$ touch flows_cred.json
....
9 Nov 16:31:12 - [warn] Existing credentials file is empty
9 Nov 16:31:12 - [warn] Encrypted credentials not found
The reason we warn if the file is missing, or empty is because we don't know if that's what the user intended or not - and could be a sign that something is wrong and the flows won't work because credentials are missing.
If you really want to get rid of the warnings, then you'll need a valid credentials file - even if the credentials in it are empty.
No-one has asked for a way to do this before, so the method is a bit convoluted.
add an HTTP Request node, tick the authentication box and enter username/password. Deploy. That will generate a valid creds file.
delete the request node and hit deploy - that will update the creds file with nothing in it - but an encrypted nothing in it.
At that point, you'll have an empty creds file for that instance of Node-RED, which has been properly encrypted for that instance.
As I said, quite convoluted, but this simply isn't a scenario anyone has asked us to do anything different with.