Dual NVMe memory module

We are planning to use two numbers of PCIe Gen3 x4 NVMe SSDs (each 2TB) along with Xavier AGX System on module.
Is it possible to do so?
Will this add any software complexity?

Yes. It should be doable.
You can use the slots M.2 Key-M & CEM-x8 slots to connect both the NVMe drives.
FWIW, you need one NVMe in M.2 Key-M form-factor and the other one in normal PCIe form-factor.
There is no additional SW complexity here. Both of them are expected to work out of the box

Is this in reference to the carrier board.
We are planning to use the AGX SOM and are designing our own carrier board. In such a case, both can be M.2 Key-M form-factor, right?
And while using the x8 controller, the remaining 4 lanes can be left unconnected?

Ok. If you are going to design a custom board, then, yes, you can have both slots in M.2 Key-M form-factor. And yes, it is Ok to leave the 4 lanes unconnected for the x8 controller.