You are talking about two different things.
NCVerilog is a simulation tool, and the FPGA is real hardware. So there will be differences. Real equipment will usually be faster, but with the simulator you can enjoy debugging. Trying to test a specific signal is just a matter of adding a line to the test wall. In addition, you can easily make changes to the simulated model instead of having to redo the FPGA.
If you run the simulation on a powerful enough machine, you can sometimes bring real performance closer (assuming FPGA is slow).
In general, you must do both. Use the simulator to complete your basic development and evaluation. Navigate your FPGA equipment as soon as your design is well defined.