Is there a way to have visibility of certain part of Nios II system memory for debug purpose?
It isn't entirely clear what kind of visibility you're looking for. For peripheral registers (or any other hardware nodes, for that matter), there's always SignalTap, the FPGA equivalent of a logic analyzer.

If you want to monitor the values of a few memory locations, you can add "shadow" registers for those locations that you can also connect to SignalTap. A shadow register is write-only latch that gets updated whenever the corresponding address on the memory address bus gets written to.