Just passing this along in case anyone else is wondering about whether it's safe to upgrade...
I finally installed OS X 10.11.1 (El Capitan) on my Mac tonight. I was a little worried that NodeBox might have some issues with the captain, but so far it appears to be running fine.
One note: I am still running an older version of Java (1.8.0_25-b17). I am afraid that using the latest Java might cause trouble and it would be a pain to go back, so am erring on the side of caution.
John