Does Backupninja support congiruration files inside subfolders?

Other
,
1

No.
The configdirectory option should be a real folder (without wildcards) because of the code:

if [ ! -d "$configdirectory" ]; then
   echo "Configuration directory '$configdirectory' not found."
   fatal "Configuration directory '$configdirectory' not found."
fi

0xacab.org/riseuplabs/backupninja/blob/backupninja_debian/1.0.1-2/src/backupninja.in#L526