Yes, Zigbee in NCS use the Zigbee shell library, which is functionally the same as Zigbee CLI in nRF5 SDK. Unlike the nRF5 SDK, where there is one specific CLI example, you can add the Zigbee shell library to any Zigbee sample in NCS, simply by configuring it. To see how to configure it in your sample, please refer to Configuring Zigbee shell. For more information about the library you can see the page Zigbee shell, where you will also find a list of Zigbee shell commands.
I believe it should work with the Zigbee shell library as well. The way the Python CLI wrapper works is that it wraps the CLI commands to Python functions, but from the device's perspective it is the same as if you send CLI commands manually in a terminal emulator. Although the Zigbee shell library in NCS works differently on the device than the CLI libraries in nRF5 SDK does, the interaction with the board from the terminal will be the same. So as long as you are using commands that are supported in the Zigbee shell library, I think it should work.
However, we have not tested using the Python CLI wrapper with NCS, so I cannot guarantee that it will work.
