I'm not sure I'm fully understanding what you mean. I guess you're looking for a config file where you can setup your default /dev directory. (never heard about a hidden directory for devices tree).
Anyway, look at /etc/udev/udev.conf, it should be something like
# The main config file for udev
# This file can be used to override some of udev's default values
# for where it looks for files, and where it places device nodes.
# udev_root - where in the filesystem to place the device nodes
udev_root="/dev/" -----> here is where you setup your default directory.
First make sure you loaded into memory the proper driver for your joystick, then if hotplug/udev do not create the node you might want to create a simple script for the purpose.
It should be something like
mknod /dev/some_node c(b) major nr minor nr
Have a look @ http://www.lanana.org/
in order you can properly setup the necessary node.
To be honest it is a problem to me telling you where you should put such script as I'm not familiar with debian and more generally with systemV scripts.
On Slack I simply added some lines required for my DVB card in /etc/udev/scripts/make_extra_nodes.sh
Hope this helps