Most of our real-time targets such as cRIO, R Series Multifunction RIO, and sbRIO targets deploy I/O from the Project Explorer.
If you are using a Real-Time PXI chassis, your non-RIO modules will not show up in the Project Explorer. You can access the channels of your device through LabVIEW VIs just like Windows-based DAQmx projects. As an example, this real-time project below has a PXI running NI Linux Real-Time, so the DAQmx module onboard (a PXIe-6375 Multifunction I/O module) is not visible from Project Explorer.
You can validate your DAQmx module and channels are connected to the LabVIEW project by adding a DAQmx Physical Channel control to your project and seeing if the module I/O appear, like the example image below.