Yes, while the documentation describes how to perform this using virtual machines, this can be done in general on real hardware. Since that HOWTO was written, there has been additional work on providing helpers for running this type of experiment, including running on PlanetLab testbed machines. This documentation describes the generalized file descriptor NetDevice, added to the ns-3.17 release: http://www.nsnam.org/docs/release/3.19/models/html/fd-net-device.html. A similar example to the one described in that HOWTO is found in the file fd-emu-udp-echo.cc.
When using emulation mode on real networks, configuration of the MAC addresses and IP addresses must be done carefully. First, the device must be able to be put into promiscuous mode. Second, the MAC address needs to be different than the hardware address of the NIC. If you intend to be riding on top of an active NIC with existing IP address (in use for other Internet traffic), you'll need to have another IP address for ns-3 that is within the right link subnet. If instead you want to dedicate the NIC to ns-3 use, then do not assign the IP address to the host NIC and just assign it to the ns-3 configuration.
The PlanetLab example also shows another configuration that uses Tap devices to send data to/from PlanetLab testbed nodes. Some of this configuration is specific to how PlanetLab works, but the use of Tap device bridged to an ns-3 device may also facilitate emulation.