HI Ian,
if you double click on them it opens their edit dialog where you can delete.
Unused nodes usually are not a problem - but it was too easy to accumulate them in your flow file without knowing they were there. This new warning (which can be ignored) is an attempt to make the user more aware of what they have.
If you imported a flow that contained a config node then just deleted the visible nodes in the workspace, that would leave the config node in place.
I think the wording needs some tuning, and the config node sidebar could be clearer - we welcome feedback on it.
Nick