I since found that there is a bug in nano < 2.7.4-1
nano: /etc/nanorc is ignored, if ~/.nanorc exists
Latest from the bug report:
I just made the dist-upgrade to Debian 9.0, which included an update of package nano to version 2.7.4-1 and the problem vanished, the bug is solved in 2.7.4-1.
The bug report: bug